Table 3. Genetic variations in LH and LL groups and shared groups.
| Variation Type | Specific LH |
Specific LL |
LH and LL |
|||
|---|---|---|---|---|---|---|
| SNP | Indel | SNP | Indel | SNP | Indel | |
| All | 801,211 | 135,149 | 682,219 | 116,233 | 1,801,636 | 56,460 |
| Intergenic | 598,300 | 102,188 | 512,803 | 28,524 | 1,385,519 | 44,249 |
| Intergenic(Upstream w/5-kb) | 39,917 | 6,311 | 33,480 | 4,894 | 77,607 | 2,371 |
| Intergenic(Downstream w/5-kb) | 39,681 | 6,361 | 33,475 | 5,815 | 78,816 | 2,446 |
| Intronic | 212,641 | 34,971 | 178,117 | 28,524 | 439,062 | 13,051 |
| 3′UTR | 3,187 | 582 | 2,396 | 449 | 5,866 | 178 |
| 5′UTR | 508 | 67 | 409 | 54 | 645 | 16 |
| Splice site | 46 | 107 | 27 | 84 | 117 | 51 |
| Splice site acceptor | 22 | 54 | 16 | 43 | 51 | 22 |
| Splice site donor | 24 | 53 | 11 | 41 | 66 | 29 |
| Start-gained | 94 | 0 | 51 | 1 | 107 | 0 |
| Start-loss | 1 | 0 | 4 | 0 | 6 | 0 |
| Stop-gained | 23 | 0 | 17 | 0 | 35 | 0 |
| Start-loss | 3 | 0 | 0 | 0 | 11 | 0 |
| Synonymous | 3,052 | NA | 2,681 | NA | 5,213 | NA |
| Nonsynonymous | 1,969 | NA | 1,656 | NA | 4,151 | NA |
| Frameshift indels | NA | 288 | NA | 200 | NA | 114 |
LH: Landrace pig group with higher backfat thickness; LL: Landrace pig group with lower backfat thickness. Specific LH: genetic variants that were only detected in LH; Specific LL: genetic variants that were only detected in LL.