Welcome to the Mouse HapMap Imputation Genotype Resource home. A high-density genotype resource of 121,433 SNPs over 94 inbred strains were collected to comprehensively understand the structure of genetic variation among laboratory mice. Combining with the 13,094 Wellcome Trust SNPs, a set of 132,285 SNPs was compiled, which we refer as to the mouse HapMap resource, which is available for download through http://www.mousehapmap.org


Using the mouse HapMap resource, it is possible to accurately impute the genotypes of the 94 strains at the 8 million SNPs discovered by the NIEHS/Perlegen mouse resequencing project. We imputed the genotypes at the NIEHS/Perlegen SNPs from the mouse HapMap SNPs and an additional set of 7,570 gap-filling SNPs provided by NIEHS/Perlegen. Since each NIEHS/Perlegen SNP probe has different quality, we classified roughly half of the SNPs as 'high-quality' SNPs, which do not have missing genotype at any of the 15 resequenced strains. The imputed genotypes are available for the high-quality SNPs, which has estimated error rate of 0.27% for high-confidence imputed genotypes. In addition, the imputed genotypes for all 8 million SNPs are also available for download. Their estimated error rate is 0.37% for high-confidence imputed genotypes. All the downloads are available through the menu bar on the left side.

64 Million Wellcome Trust SNPs

Using the same basic framework, we recently added a set of over 64 million SNPs to our resource. The Wellcome Trust Institute has resequenced 17 inbred mouse strains and has identified a large number of SNPs. We utilized this high density set of SNPs, in order to impute SNPs in the remaining 78 strains. Our final set of imputed data contains SNP calls for 94 strains over 64 million SNPs.

For the technical assistance, please contact Nick Furlotte For general correspondence on this material, please contact Eleazar Eskin or Mark Daly.

Part of this research is funded by a contract from the NIEHS. The program officer from the contract, Frank Johnson, is a co-author on this work and has been involved in the study design of the Mouse Resequencing Resource which is used in our study. Other than that, the remaining funders had no role in study design, data collection and analysis, decision to publish, or preparation of this material.