Table 1 Number of SNPs by annotation class and genome region: autosomes, X chromosome non-pseudoautosomal region (NPAR) and X pseudoautosomal region (PAR)
From: Dissecting structural and nucleotide genome-wide variation in inbred Iberian pigs
Consequence | Autosomes Guadyerbas | Autosomes Iberian pool | NPAR Guadyerbas | NPAR Iberian pool | PAR Guadyerbas | PAR Iberian pool |
|---|---|---|---|---|---|---|
Essential splice site | 30 | 30 | 1 | 1 | 0 | 0 |
Stop gained | 44 | 11 | 2 | 0 | 0 | 0 |
Stop gained,splice site | 1 | 0 | 0 | 0 | 0 | 0 |
Stop lost | 4 | 15 | 0 | 0 | 0 | 0 |
Non synonymous coding | 2650 | 1222 | 40 | 28 | 1 | 0 |
Non synonymous coding,splice site | 51 | 31 | 0 | 1 | 0 | 0 |
Synonymous coding,splice site | 49 | 24 | 3 | 0 | 0 | 0 |
Splice site,intronic | 282 | 254 | 10 | 8 | 0 | 1 |
5prime utr,splice site | 1 | 1 | 0 | 0 | 0 | 0 |
3prime utr,splice site | 2 | 0 | 0 | 0 | 0 | 0 |
Within non coding gene,splice site | 7 | 1 | 0 | 0 | 0 | 0 |
Synonymous coding | 2676 | 1611 | 33 | 34 | 0 | 1 |
Coding unknown | 8 | 4 | 0 | 0 | 0 | 0 |
Within mature mirna | 1 | 1 | 0 | 2 | 0 | 0 |
5prime utr | 193 | 418 | 0 | 7 | 0 | 0 |
3prime utr | 2103 | 1357 | 23 | 19 | 0 | 0 |
Intronic | 148468 | 78279 | 1867 | 1204 | 133 | 147 |
Within non coding gene | 286 | 99 | 12 | 3 | 0 | 0 |
Within non coding gene,intronic | 6 | 3 | 0 | 0 | 0 | 0 |
Upstream | 34314 | 15216 | 426 | 346 | 20 | 16 |
Downstream | 34395 | 15737 | 628 | 346 | 24 | 14 |
Intergenic | 433720 | 150572 | 7161 | 3620 | 3087 | 1214 |
Total | 659291 | 264886 | 10206 | 5619 | 3265 | 1393 |