Table 2 Annotation of SNPs in the Quarter Horse genome
From: Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare
| Â | Total | Homozygous | Heterozygous | Novel | Ensembl Genes |
|---|---|---|---|---|---|
All SNPs | 3,157,093 | 1,293,374 | 1,863,719 | 2,814,367 | 24,023 |
   Intergenic | 2,224,292 | 908,169 | 1,316,123 | 1,991,041 | 19,644 |
   Intergenic (Upstream w/in 1 kb) | 40,948 | 19,241 | 21,707 | 37,566 | 12,803 |
   Intergenic (Downstream w/in 1 kb) | 31,901 | 13,327 | 18,574 | 28,494 | 10,580 |
   Intergenic (Up/Down w/in 1 kb) | 929 | 427 | 502 | 866 | 399 |
   Genic | 859,023 | 352,210 | 506,813 | 756,400 | 19,414 |
Intron | 811,204 | 332,455 | 478,749 | 712,764 | 14,778 |
Non-Coding Exon | 5,935 | 2,019 | 3,916 | 5,575 | 2,123 |
5' UTR | 1,734 | 1,014 | 720 | 1,630 | 1,049 |
3' UTR | 1,821 | 780 | 1,041 | 1,594 | 1,184 |
Intron Splice Site | 300 | 185 | 115 | 280 | 276 |
Exon Splice Site | 657 | 320 | 337 | 593 | 595 |
Coding Exon | 37,372 | 15,437 | 21,935 | 33,964 | 10,485 (305 imprinted) |
Synonymous | 19,667 | 7,626 | 12,041 | 17,699 | 7,982 |
Stop Gain | 214 | 50 | 164 | 206 | 190 |
Stop Loss | 8 | 5 | 3 | 7 | 8 |
Non-Synonymous | 18,140 | 8,076 | 10,064 | 16,645 | 6,899 |