Horse Single Nucleotide Polymorphisms

Paired-end low-coverage whole genome shotgun reads were generated from 7 breeds (Arabian, Andalusian, Akhal-teke, Quarterhorse, Icelandic horse, Standardbred and Thoroughbred - 100,000 each). The WGS reads were placed uniquely on the Equus1.0 Thoroughbred assembly and SNP detection was carried out by SSAHA-SNP. The validation rate for these SNPs is estimated at approximately 95%. A second set of SNPs were discovered by comparing reads in the WGA assembly. SNPs were defined as mismatch positions that had a base quality of >= 30 on both reads in a region that aligned without gaps, and with at most one additional mismatch in the ten flanking bases.

Both sets include 948,609 SNPs in total distributed across chromosomes 1-31 and X. SNPs falling on contigs that are not assigned to chromosomes are excluded from this set. http://www.broadinstitute.org/ftp/distribution/horse_snp_release/v2

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File Name SNPs Included
horse_chr1_over100mb.xls 43,603
horse_chr1_snps_All.xls 65.537horse_chr1_snps_All.txt 86,038
horse_chr1_under100mb.xls 42,435
horse_chr2_snps.xls 54,561
horse_chr3_snps.xls 41,095
horse_chr4_snps.xls 38,594
horse_chr5_snps.xls 34,450
horse_chr6_snps.xls 37,443
horse_chr7_snps.xls 40,476
horse_chr8_snps.xls 41,193
horse_chr9_snps.xls 37,574
horse_chr10_snps.xls 36,972
horse_chr11_snps.xls 30,067
horse_chr12_snps.xls 14,987
horse_chr13_snps.xls 12,829
horse_chr14_snps.xls 39,313
horse_chr15_snps.xls 45,828
horse_chr16_snps.xls 38,826
horse_chr17_snps.xls 19,591
horse_chr18_snps.xls 18,098
horse_chr19_snps.xls 24,202
horse_chr20_snps.xls 30,607
horse_chr21_snps.xls 25,862
horse_chr22_snps.xls 26,430
horse_chr23_snps.xls 14,436
horse_chr24_snps.xls 24,243
horse_chr25_snps.xls 19,311
horse_chr26_snps.xls 20,239
horse_chr27_snps.xls 22,675
horse_chr28_snps.xls 22,077
horse_chr29_snps.xls 17.335
horse_chr30_snps.xls 10,560
horse_chr31_snps.xls 11,670
horse_chrX_snps.xls 11,063