SQLite database of variants in CC founder mouse strains (build 39)

SQLite databases of variants in the founder mouse strains for the Collaborative Cross and Diversity Outbred mice, for use with R/qtl2.

fv.2021.snps.db3 uses mouse genome build 39.

Each contains 6 tables: csqs, genes, meta, snps, so_terms, variants.

The variants table has fields variants_id, chr, pos, sdp (strain distribution pattern), ref (reference allele), alt (alt allele), confidence, sample_* (genotype for each of the 8 founder strains), conf_* (confidence for each of the 8 founder strains), and max_csq.

The snps table is similar but with a reduced set of fields: snp_id, chr, pos_Mbp, alleles, sdp, ensemble_gene_id, csq.

The genes table has fields ensembl_id, ensembl_version, symbol, name, chromosome, start_position, end_position, strand.

The meta table has meta-data information on the source of the data.

The source for the variants is Sanger: https://www.mousegenomes.org/snps-indels/

See also the web interface to these databases: https://churchilllab.jax.org/foundersnps/search