Table 2 Number of effects by private and shared SNPs detected by next generation sequencing of five horses
SNPEff terms by type | Shared (all 5 horses) | Duelmener | Sorraia | Arabian | Hanoverian (two horses) |
|---|---|---|---|---|---|
Downstream | 89229 | 43289 | 34418 | 31295 | 13056 |
Exon | 1728 | 694 | 494 | 48 | 192 |
Intergenic | 1313808 | 711015 | 549696 | 487818 | 207619 |
Intron | 451550 | 256400 | 199575 | 180419 | 79926 |
Non-synonymous coding | 9507 | 3053 | 2367 | 2191 | 878 |
Non-synonymous start | 7 | 0 | 0 | 0 | 0 |
Splice site acceptor | 159 | 15 | 10 | 11 | 3 |
Splice site donor | 260 | 23 | 19 | 16 | 7 |
Start gained | 159 | 57 | 43 | 17 | 10 |
Start lost | 15 | 0 | 0 | 0 | 0 |
Stop gained | 48 | 36 | 28 | 29 | 16 |
Stop lost | 8 | 1 | 2 | 0 | 2 |
Synonymous coding | 8138 | 3883 | 3030 | 2686 | 1198 |
Synonymous start | 1 | 0 | 0 | 0 | 0 |
Synonymous stop | 1 | 4 | 4 | 1 | 1 |
Upstream | 113982 | 45203 | 36447 | 32191 | 13289 |
3‘UTR | 1240 | 607 | 488 | 437 | 191 |
5‘UTR | 1682 | 243 | 178 | 165 | 76 |
total | 1584011 | 810687 | 824072 | 737324 | 316464 |