Reduced Representation Libraries from DNA Pools Analysed with Next Generation Semiconductor Based-Sequencing to Identify SNPs in Extreme and Divergent Pigs for Back Fat Thickness

Table 2

Summary of the SNP annotation results obtained using the variant effect predictor (VEP) tool.

Gene position or SNP effect	Number of SNPs
3 prime UTR variant	203
3 prime UTR variant, NMD transcript variant	1
5 prime UTR variant	58
Downstream gene variant	2710
Intergenic variant	24414
Intron variant	12591
Intron variant, NMD transcript variant	126
Intron variant, noncoding transcript variant	306
Missense variant	159
Missense variant, splice region variant	8
Noncoding transcript exon variant, noncoding transcript variant	29
Splice acceptor variant	2
Splice donor variant	1
Splice region variant, 3 prime UTR variant	1
Splice region variant, intron variant	25
Splice region variant, synonymous variant	12
Stop gained	2
Stop lost	1
Stop retained variant	1
Synonymous variant	217
Synonymous variant, NMD transcript variant	3
Upstream gene variant	2675
Total	43545

The sum includes 39,165 variations, 4,380 of which have multiple annotations, for a total of 43,545 SNP annotations.