Genomic variation

For a number of genomes, Ensembl Genomes provides genomic variation data, 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.

Ensembl Genomes uses the Ensembl variation platform for data storage and display/dissemination, allowing variation data to be accessed using the REST and Perl APIs and BioMart.

For a complete list of genomes with variation data provided by Ensembl Genomes, please visit this page.