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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.

Original publication




Journal article



Publication Date





289 - 294


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


Animals, Mice, Inbred Strains, Mice, Inbred C57BL, Animals, Laboratory, Mice, Genomics, Phylogeny, Gene Expression Regulation, Phenotype, Alleles, Quantitative Trait Loci, Genome, Genetic Variation