Table 5 SNP functional class membership
From: Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery
Functional class | Holstein | Black Angus | Intersection | Union |
|---|---|---|---|---|
Intergenic | 2,488,430(66.3) | 2,131,566(65.7) | 1,124,055(65.6) | 3,495,941(66.1) |
Intronic | 1,003,805(26.7) | 881,566(27.2) | 469,082(27.4) | 1,416,289(26.8) |
Upstream | 116,529(3.1) | 103,589(3.2) | 53,027(3.1) | 167,091(3.2) |
Downstream | 104,762(2.8) | 90,788(2.8) | 48,128(2.8) | 147,422(2.8) |
Synonymous coding | 16,161(0.4) | 15,102(0.5) | 8,051(0.5) | 23,212(0.4) |
Nonsynonymous coding | 11,598(0.3) | 10,723(0.3) | 5,490(0.3) | 16,831(0.3) |
3' UTR | 8,732(0.2) | 7,753(0.2) | 4,200(0.2) | 12,285(0.2) |
Splice sitea | 2,921(0.1) | 2,679(0.1) | 1,421(0.1) | 4,179(0.1) |
5' UTR | 1,591(0.0) | 1,382(0.0) | 680(0.0) | 2,293(0.0) |
Within non coding gene | 791(0.0) | 763(0.0) | 344(0.0) | 1210(0.0) |
Essential splice siteb | 197(0.0) | 166(0.0) | 94(0.0) | 269(0.0) |
Stop gained | 126(0.0) | 124(0.0) | 46(0.0) | 204(0.0) |
Stop lost | 13(0.0) | 8(0.0) | 5(0.0) | 16(0.0) |
Within mature miRNA | 7(0.0) | 2(0.0) | 1(0.0) | 8(0.0) |
Total | 3,755,663(100) | 3,246,211(100) | 1,714,624(100) | 5,287,250(100) |