Table 3.
Distribution of SnpEff annotation InDel variants in three cattle breeds.
| Fields | LQ | WN | WS |
|---|---|---|---|
| Total number | 2,153,542 | 2,586,758 | 2,471,063 |
| 3 prime UTR | 54,892 | 67,465 | 65,837 |
| 5 prime UTR | 9904 | 12,229 | 12,421 |
| Bidirectional gene fusion | 80 | 83 | 139 |
| Conservative inframe deletion | 561 | 814 | 1021 |
| Conservative inframe insertion | 434 | 546 | 781 |
| Disruptive inframe deletion | 1039 | 1292 | 1735 |
| Disruptive inframe insertion | 483 | 583 | 955 |
| Downstream gene | 585,215 | 719,779 | 693,994 |
| Frameshift variant | 4168 | 5516 | 9559 |
| Gene fusion | 198 | 178 | 232 |
| Intergenic region | 1152,941 | 1,382,145 | 1,318,068 |
| Intragenic | 1,485,117 | 1,817,239 | 1,775,709 |
| Intron | 9,407,833 | 11,108,642 | 10,992,364 |
| Non coding transcript exon | 17,425 | 21,355 | 21,201 |
| Non coding transcript | 3,688,414 | 4,441,858 | 4,170,309 |
| Splice acceptor | 384 | 451 | 471 |
| Splice donor | 368 | 412 | 477 |
| Splice region | 6396 | 7787 | 8542 |
| Start lost | 58 | 64 | 54 |
| Stop gained | 57 | 73 | 131 |
| Stop lost | 32 | 73 | 61 |
| Upstream gene | 54,6024 | 666,968 | 642,273 |