Ensembl Genomes provides genomic variation data for a number of genomes, including single nucleotide polymorphisms(SNPs) and insertion-deletion mutations (indels) from various sources, for which any effects on transcripts in the area are calculated.
In Ensembl Genomes variant data is imported from dbSNP, sequencing centers (e.g. the Broad Institute) and from a range of third parties. The exact source of variant data is provided on the information page for each genome in the Ensembl browser (e.g. A. thaliana). Variant data is usually obtained in VCF format and imported using the Ensembl VCF import pipeline. For some species, resequencing data is obtained from the European Nucleotide Archive (ENA) Short Read Archive (SRA) and aligned to the reference genomes using a short-read sequence alignment pipeline.
For a complete list of genomes with variation data provided by Ensembl Genomes, please visit Genomes with genomic variation data.