Mouse Genomes Project - Query SNPs, indels or SVs

Select a gene or region in the pane to the right.

Please note that all variation consequences are calculated with the VEP on a per-site basis and do not take into account any other variants present on the same transcript.

Further information

Full datasets are available via our FTP site:


  • Mouse genomic variation and its effect on phenotypes and gene regulation.

    Keane TM, Goodstadt L, Danecek P, White MA, Wong K, Yalcin B, Heger A, Agam A, Slater G, Goodson M, Furlotte NA, Eskin E, Nellåker C, Whitley H, Cleak J, Janowitz D, Hernandez-Pliego P, Edwards A, Belgard TG, Oliver PL, McIntyre RE, Bhomra A, Nicod J, Gan X, Yuan W, van der Weyden L, Steward CA, Bala S, Stalker J, Mott R, Durbin R, Jackson IJ, Czechanski A, Guerra-Assunção JA, Donahue LR, Reinholdt LG, Payseur BA, Ponting CP, Birney E, Flint J and Adams DJ

    The Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1HH, UK.

    We report genome sequences of 17 inbred strains of laboratory mice and identify almost ten times more variants than previously known. We use these genomes to explore the phylogenetic history of the laboratory mouse and to examine the functional consequences of allele-specific variation on transcript abundance, revealing that at least 12% of transcripts show a significant tissue-specific expression bias. By identifying candidate functional variants at 718 quantitative trait loci we show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus. These sequences provide a starting point for a new era in the functional analysis of a key model organism.

    Funded by: Biotechnology and Biological Sciences Research Council: BB/F022697/1; Cancer Research UK: A6997; Medical Research Council: G0800024, MC_EX_G0802457, MC_U127561112, MC_U137761446; NHGRI NIH HHS: T32 HG002536; NHLBI NIH HHS: K25 HL080079; NIAID NIH HHS: N01AI15416; NLM NIH HHS: 2T15LM007359, T15 LM007359; Wellcome Trust: 077192, 079912, 082356, 083573, 083573/Z/07/Z, 085906, 085906/Z/08/Z, 090532

    Nature 2011;477;7364;289-94

  • Sequence-based characterization of structural variation in the mouse genome.

    Yalcin B, Wong K, Agam A, Goodson M, Keane TM, Gan X, Nellåker C, Goodstadt L, Nicod J, Bhomra A, Hernandez-Pliego P, Whitley H, Cleak J, Dutton R, Janowitz D, Mott R, Adams DJ and Flint J

    The Wellcome Trust Centre for Human Genetics, Roosevelt Drive, Oxford OX3 7BN, UK.

    Structural variation is widespread in mammalian genomes and is an important cause of disease, but just how abundant and important structural variants (SVs) are in shaping phenotypic variation remains unclear. Without knowing how many SVs there are, and how they arise, it is difficult to discover what they do. Combining experimental with automated analyses, we identified 711,920 SVs at 281,243 sites in the genomes of thirteen classical and four wild-derived inbred mouse strains. The majority of SVs are less than 1 kilobase in size and 98% are deletions or insertions. The breakpoints of 160,000 SVs were mapped to base pair resolution, allowing us to infer that insertion of retrotransposons causes more than half of SVs. Yet, despite their prevalence, SVs are less likely than other sequence variants to cause gene expression or quantitative phenotypic variation. We identified 24 SVs that disrupt coding exons, acting as rare variants of large effect on gene function. One-third of the genes so affected have immunological functions.

    Funded by: Cancer Research UK: 13031; Medical Research Council: G0800024, MC_EX_G0802457, MC_U137761446; Wellcome Trust: 079912, 082356, 090532, 098051

    Nature 2011;477;7364;326-9





e.g. Cops5



e.g. 10:10000000-10001000

SNP/Indel types

All None


Structural variant types

All None



All None DO/CC founders