Table 3.
Effects of putative SNPs
| SNP effect | After filtration | Joined with gene expression results | ||
|---|---|---|---|---|
| Landrace | Duroc | Landrace | Duroc | |
| 3’UTR | 17,741 | 17,715 | 573 | 627 |
| 5’UTR | 3622 | 3691 | 62 | 102 |
| Frameshift | 453 | 516 | 3 | 12 |
| Missense | 9946 | 10,424 | 267 | 246 |
| Splice acceptor | 16 | 17 | 0 | 0 |
| Splice donor | 12 | 12 | 0 | 0 |
| Splice site region | 338 | 362 | 3 | 7 |
| Start lost | 13 | 8 | 1 | 0 |
| Stop gained | 68 | 63 | 0 | 3 |
| Stop lost | 27 | 34 | 0 | 2 |
| Synonymous | 21,060 | 21,273 | 610 | 731 |
| SNP impact | ||||
| High | 600 | 663 | 4 | 17 |
| Moderate | 10,006 | 10,486 | 269 | 250 |
| Low | 21,974 | 22,200 | 623 | 752 |
| Modifier | 23,251 | 23,293 | 676 | 807 |
SNP effect according to SnpEff for putative polymorphisms detected in Landrace and Duroc. The results presented are after filtration and joined with differentially expressed genes. Some SNPs have more than one predicted effect