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
| File Name | SNPs Included |
|---|---|
| horse_chr1_over100mb.xls | 43,603 |
| 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 |
