Imputed Genotype Resource - 74 inbred mouse strains (Szatkiewicz et al. 2008) (build 37)

Description

We have created a high-density SNP resource encompassing 7.87 million polymorphic loci across 74 inbred mouse strains of the laboratory mouse by combining data available from public databases and training a hidden Markov model to impute missing genotypes in the combined data. The strong linkage disequilibrium found in dense sets of SNP markers in the laboratory mouse provides the basis for accurate imputation. Using genotypes from eight independent SNP resources, we empirically validated the quality of the imputed genotypes and demonstrated that they are highly reliable for most inbred strains. The imputed SNP resource will be useful for studies of natural variation and complex traits. It will facilitate association study designs by providing high-density SNP genotypes for large numbers of mouse strains. We anticipate that this resource will continue to evolve as new genotype data become available for laboratory mouse strains.

Data

[ Previous Datasets (Mouse Genome Build 36) ]
Mouse Genome Build 37
Strains

• 129S1/SvImJ
• 129S4/SvJae
• 129X1/SvJ
• A/J
• AKR/J
• BALB/cByJ
• BALB/cJ
• BPH/2J
• BPL/1J
• BPN/3J
• BTBR T<+> tf/J
• BUB/BnJ
• C3H/HeJ
• C57BL/10J
• C57BL/6J
• C57BLKS/J
• C57BR/cdJ
• C57L/J
• C58/J
• CALB/RK
• CAST/EiJ
• CBA/J
• CE/J
• CZECHII/EiJ
• DBA/1J
• DBA/2J
• DDK/Pas
• DDY/JCLSIDSEYFRKJ
• EL/SUZ_2
• FVB/NJ
• HTG/GOSFSN
• I/LnJ
• ILS
• IS/CAMRK
• ISS
• JF1/Ms
• KK/HLJ
• LEWES/EI
• LG/J
• LP/J
• MA/MyJ
• MAI/Pas
• MOLF/EiJ
• MOLG/DN
• MRL/MpJ
• MSM/Ms
• NOD/LtJ
• NON/LtJ
• NOR/LTJ
• NZB/BlNJ
• NZO/HlLtJ
• NZW/LacJ
• O20
• P/J
• PERA/EiJ
• PERC/EI
• PL/J
• PWD/Ph
• PWK/PhJ
• Qsi5
• RF/J
• RIIIS/J
• SEA/GnJ
• SEG/Pas
• SJL/J
• SKIVE/EI
• SM/J
• SOD1/EI
• SPRET/EiJ
• ST/bJ
• SWR/J
• TALLYHO/JNGJ
• WSB/EiJ
• ZALENDE/EiJ

SNP Genotype Data (Mouse Genome Build 37)
Upper case letters indicate experimental genotypes; lower case letters indicate imputed genotypes.

SNP Confidence Scores for all (Mouse Genome Build 37)
For every genotype, imputed and experimental, a confidence score is computed as the posterior probability under the trained HMM.

SNP Genotype Confidence Scores (Mouse Genome Build 37)
For the imputed genotypes only

Publications

Szatkiewicz JP, Beane GL, Ding Y, Hutchins L, Pardo-Manuel de Villena F, Churchill GA
Mamm Genome. 2008 Mar;19(3):199-208 [ Full Text ] PMCID: PMC2725522  [ data build 36 ]