GoatVar

Welcome to GGVD

Goats are one of the most widespread and economically important farmed animals, which number ~1 billion in population and in ~579 breeds. Goats inhabit a wide agroecological niche spanning all continents and supply milk, meat, and fiber for human consumption. Here, we developed a comprehensive Goat Genome Variation and Selective Signatures Database (GGVD) for providing five main functionalities: Variation Search, Genomic Signature Search, Genome Browser, Alignment Search Tools (BLAT/BLAST) and Genome Coordinate Conversion Tool (LiftOver). In current version, GGVD contains 41,439,258 SNPs and 5,136,295 indels derived from 232 worldwide resequencing samples. And selective signatures for domestication and each representative groups were evaluated by using eight methods (Pi, Hp, Tajima’s D, CLR, iHS, FST, Pi ratio and XP-EHH). GGVD will be a useful archive for in-depth analysis in goat breeding.


Features

  • Basic information of 232 worldwide goat accessions.
  • We provide two ways to view SNPs and indels, one is interactive tables and visual map that project the allele frequency distribution pattern in 20 geographically distributed goat populations and eight subgroups according to PCA and NJ tree, and the other is Gbrowse format.
  • We provide a parallel search for variations, such as variant rsid, gene symbol, and genomic region.
  • We provide selection scores for 10 groups, including Bezoars, African goats, African dairy goats, European goats, Australian goats, Southwest Asian goats, South Asian goats, East Asian goats, Tibetan goats, and Bezoars Vs Domesitc goats, by using eight statistical terms.
  • We integrate variations, selection scores, gene annotation, and conserved elements into Gbrowse to facilitate global presentation.


Bezoar: 24
Africa: 54
Africa_dairy_goat: 16
Europe: 31
Australia: 5
Southwest_Asia: 36
South_Asia: 9
East_Asia: 57