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

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.

Reference

An imputed genotype resource for the laboratory mouse.
Szatkiewicz JP, Beane GL, Ding Y, Hutchins L, Pardo-Manuel de Villena F, Churchill GA.
Mamm Genome. 2008 Mar;19(3):199-208. PMCID: PMC2725522 [ Full Text ]

Datasets - Mouse Genome Build 37


[ Previous Datasets (Mouse Genome Build 36) ]


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.

Chromosome 1 Download zip file (19.3MB)
Chromosome 2 Download zip file (13.9MB)
Chromosome 3 Download zip file (14.5MB)
Chromosome 4 Download zip file (12.5MB)
Chromosome 5 Download zip file (13.8MB)
Chromosome 6 Download zip file (13.7MB)
Chromosome 7 Download zip file (11.5MB)
Chromosome 8 Download zip file (12.4MB)
Chromosome 9 Download zip file (10.3MB)
Chromosome 10 Download zip file (10.7MB)
Chromosome 11 Download zip file (7.2MB)
Chromosome 12 Download zip file (11.3MB)
Chromosome 13 Download zip file (10.9MB)
Chromosome 14 Download zip file (9.9MB)
Chromosome 15 Download zip file (9.7MB)
Chromosome 16 Download zip file (8.4MB)
Chromosome 17 Download zip file (7.8MB)
Chromosome 18 Download zip file (8.1MB)
Chromosome 19 Download zip file (6.3MB)
Chromosome X Download zip file (5.4MB)
Duplicate SNPs Download zip file (52KB)


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.

Chromosome 1 Download zip file (91.6MB)
Chromosome 2 Download zip file (64MB)
Chromosome 3 Download zip file (67MB)
Chromosome 4 Download zip file (61.7MB)
Chromosome 5 Download zip file (64.5MB)
Chromosome 6 Download zip file (66MB)
Chromosome 7 Download zip file (52.6MB)
Chromosome 8 Download zip file (53.6MB)
Chromosome 9 Download zip file (48.2MB)
Chromosome 10 Download zip file (51.2MB)
Chromosome 11 Download zip file (33.8MB)
Chromosome 12 Download zip file (53.8MB)
Chromosome 13 Download zip file (50.3MB)
Chromosome 14 Download zip file (42.8MB)
Chromosome 15 Download zip file (44.7MB)
Chromosome 16 Download zip file (40.1MB)
Chromosome 17 Download zip file (37.2MB)
Chromosome 18 Download zip file (38.1MB)
Chromosome 19 Download zip file (29.9MB)
Chromosome X Download zip file (28.5MB)
Duplicate SNPs Download zip file (196KB)


SNP Genotype Confidence Scores (Mouse Genome Build 37)

For the imputed genotypes only

Chromosome 1 Download zip file (79.2MB)
Chromosome 2 Download zip file (55.2MB)
Chromosome 3 Download zip file (57.8MB)
Chromosome 4 Download zip file (54MB)
Chromosome 5 Download zip file (55.3MB)
Chromosome 6 Download zip file (57.2MB)
Chromosome 7 Download zip file (45.1MB)
Chromosome 8 Download zip file (45.7MB)
Chromosome 9 Download zip file (41.2MB)
Chromosome 10 Download zip file (44.2MB)
Chromosome 11 Download zip file (29.4MB)
Chromosome 12 Download zip file (46.3MB)
Chromosome 13 Download zip file (42.8MB)
Chromosome 14 Download zip file (36.5MB)
Chromosome 15 Download zip file (38.4MB)
Chromosome 16 Download zip file (34.6MB)
Chromosome 17 Download zip file (31.9MB)
Chromosome 18 Download zip file (32.7MB)
Chromosome 19 Download zip file (25.6MB)
Chromosome X Download zip file (25.1MB)