PigVar

The Pig variations and Positive Selection (PigVar) database is a data repository that focuses on the variation information (SNPs and structural variations (SVs)) and selection signatures of pigs and their outgroup genomes. In current version, PigVar contains 64.6 and 36.8 million non-redundant SNPs derived from 280 pigs and 7 outgroups respectively. PigVar also contains 7,236,813 SVs of Asian-origin pigs. With its functionalities for browsing for SNPs and search for other Variations with their selection scores, PigVar provides an important public access resource to the research community to facilitate the study of pig’s artificial and natural selection, as well as phenotypic diversity.

• Non-redundant SNP dataset for European and Asian pigs, and their outgroups are provided in this database.
• Structural variations (SVs) of Asian pigs are provided in PigVar database.
• We provide two ways to view SNPs, one is table-based format and the other is GBrowse format.
• We also provide search functions able to get SNPs and SVs in a genome region, and in an individual sample.
• We provide detailed information for each variation, including original sample, chromosome position, 3’ and 5’ flanking sequences, variation annotation in protein-coding or lincRNA gene.
• A comparative function is provided to facilitate comparison of SNPs in different samples.
• We provide the selection score for Chinese domestic pigs, European domestic pigs and Tibetan pigs using five statistical terms.
• The SNP files calling by GATK and samtools mpileup, phased SNPs and SVs in vcf format are provided in the download ftp. Users can download the data and perform deeper analysis.