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 database (GGVD) dedicated to variations, selective signatures and introgression regions from modern and ancient goat genomes. GGVD provides seven main functionalities: Genomic Signature Search, Introgression Browse, Variation Search, Genome Browser, Alignment Search Tools (BLAT/BLAST), A Genome Coordinate Conversion Tool (LiftOver), and A Genome Selective Signature Scans Tool (pcadapt). Users can freely visualize the frequency of genomic variations in geographical maps, selective regions in interactive tables, Manhattan plots or line charts, and especially, the SNP genotype patterns in heatmaps. GGVD allows users to identify breeding-associated candidate genes and variants, and track the state of variants before, during and following selection and introgression events.

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Features

  • Basic information of 208 modern domestic goats, 24 bezoars, 46 ibex, and 82 ancient goats.
  • We provide two ways to view SNPs and indels, one is interactive tables and geographical maps, and the other is Gbrowse format.
  • We provide selection scores for 16 groups, including Bezoars, African goats, African dairy goats, European goats, Australian goats, Southwest Asian goats, South Asian goats, East Asian goats, Tibetan goats, Toggenburg goats, Saanen goats, Longlin goats, Leizhou goats, Cashmere goats, Beetal goats, and Bezoars vs. Domestic goats, by using eight statistical terms.
  • We provide introgressed regions and haplotypes of all samples to help identify the most likely source of species and lineages.
  • We integrate variations, selection scores, genotype patterns, gene annotation, and conserved elements into Gbrowse to facilitate global presentation.
Construction pipeline
Neighbor-joining tree
Sample Geographic Distribution >> Modern goats
Bezoar
Africa
Africa (Dairy)
Europe
Australia
Southwest Asia
South Asia
East Asia