Table 1 Summary and annotation of SNPs in Berkshire pigs

From: Whole-genome sequencing of Berkshire (European native pig) provides insights into its origin and domestication

Category

Number of SNPs

Total

3,645,294

Upstream

23,796

Exonic

Missense

7,713

 

Stop gain

44

 

Stop loss

16

 

Synonymous

14,132

Intronic

792,471

Splicing

118

Downstream

23,597

Upstream/Downstream

243

Intergenic

2,783,164

  1. The package ANNOVAR56 was used to identify whether SNPs cause protein coding changes and amino acids that are affected. ‘Upstream’ refers to a variant that overlaps with the 1 kb region upstream of the gene start site. ‘Stop gain’ means that an nsSNP leads to the creation of a stop codon at the variant site. ‘Stop loss’ means that an nsSNP leads to the elimination of a stop codon at the variant site. ‘Splicing’ means that a variant is within 2 bp of a splice junction. ‘Downstream’ means that a variant overlaps with the 1 kb region downstream of the gene end site. ‘Upstream/Downstream’ means that a variant is located in downstream and upstream regions (possibly for two different genes).
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