GenomeMUSter is a comprehensive SNP data resource that includes typed, sequenced, and imputed genotypes of 657 inbred mouse strains and their derivatives across chromosomes 1-19, X, Y, and Mt. Genotypes from ten legacy datasets available from MPD, the Sanger REL2004 and REL1505, whole genome sequencing of the Collaborative Cross (CC), BXD recombinant inbred strains and C57BL/6J Eve (B6Eve), and long read whole genome sequencing of 42 inbred strains were merged by chromosome and within chromosome in 10 Mb segmented regions. The table of results displays the requested data from GenomeMUSter API combined with functional annotation data from MVAR (Mouse Variation Registry).
When there were disagreements regarding the genotype call for a strain and position, the consensus vote across all datasets was used. Genotypes were removed and imputed if no consensus was reached unless the disagreement was complementary, e.g., A and T. Once the datasets were merged and harmonized, missing genotypes were imputed for each strain in each 10Mb region.
The confidence level for known genotypes is 1 and between 0 and 1 for imputed genotypes. The confidence level represents the strain-specific accuracy on the held-out test set in each 10Mb region.
Genotypes were imputed using the Viterbi algorithm, as implemented in HaploQA (Github repository)
GRCm39 coordinates provided by pyliftover v0.4
Please use RRID:SCR_024214 when citing GenomeMUSter
Ball RL, Bogue MA, Liang H, Srivastava A, Ashbrook DG, Lamoureux A, Gerring MW, Hatoum AS, Kim MJ, He H, Emerson J, Berger AK, Walton DO, Sheppard K, El Kassaby B, Castellanos F, Kunde-Ramamoorthy G, Lu L, Bluis J, Desai S, Sundberg BA, Peltz G, Fang Z, Churchill GA, Williams RW, Agrawal A, Bult CJ, Philip VM, Chesler EJ. GenomeMUSter mouse genetic variation service enables multitrait, multipopulation data integration and analysis. Genome Res. 2024 Feb 7;34(1):145-159. doi: 10.1101/gr.278157.123. PMID: 38290977; PMCID: PMC10903950.
Arslan A, Fang Z, Wang M, Tan Y, Cheng Z, Chen X, Guan Y, Pisani LJ, Yoo B, Bejerano G, Peltz G. Analysis of structural variation among inbred mouse strains. BMC Genomics 24, 97 (2023). https://doi.org/10.1186/s12864-023-09197
Ashbrook DG, Sasani T, Maksimov M, Gunturkun MH, Ma N, Villani F, Ren Y, Rothschild D, Chen H, Lu L, Colonna V, Dumont B, Harris K, Gymrek M, Pritchard JK, Palmer AA, Williams RW. Private and sub-family specific mutations of founder haplotypes in the BXD family reveal phenotypic consequences relevant to health and disease. bioRxiv 2022.04.21.489063; doi: https://doi.org/10.1101/2022.04.21.489063
Attie AD, Churchill GA, Petkov P, Sullivan PF, Brennan JR, McMillan L, Pardo-Manuel de Villena F. The Mouse Universal Genotyping Array: From Substrains to Subspecies. G3 (Bethesda). 2015 Dec 18;6(2):263-79. doi: 10.1534/g3.115.022087.
Eskin E. SNP data, 132,000+ locations for 248 inbred and RI strains of mice. MPD:UCLA1. Mouse Phenome Database web resource (RRID:SCR_003212), The Jackson Laboratory, Bar Harbor, Maine USA. https://phenome.jax.org [Cited (date)]
Frazer KA, Eskin E, Kang HM, Bogue MA, Hinds DA, Beilharz EJ, Gupta RV, Montgomery J, Morenzoni MM, Nilsen GB, Pethiyagoda CL, Stuve LL, Johnson FM, Daly MJ, Wade CM, Cox DR. A sequence-based variation map of 8.27 million SNPs in inbred mouse strains. Nature. 2007 Aug 30;448(7157):1050-3. Epub 2007 Jul 29.
Keane TM, Goodstadt L, Danecek P, White MA, Wong K et al. Mouse genomic variation and its effect on phenotypes and gene regulation. Nature 2011;477;7364;289-94
Kirby A, Kang HM, Wade CM, Cotsapas C, Kostem E, Han B, Furlotte N, Kang EY, Rivas M, Bogue MA, Frazer KA, Johnson FM, Beilharz EJ, Cox DR, Eskin E, Daly MJ. Fine mapping in 94 inbred mouse strains using a high-density haplotype resource. Genetics. 2010 Jul;185(3):1081-95. Epub 2010 May 3.
McLaren W, Gil L, Hunt SE, Riat HS, Ritchie GR, Thormann A, Flicek P, Cunningham F. The Ensembl Variant Effect Predictor. Genome Biology Jun 6;17(1):122. (2016). https://useast.ensembl.org/info/docs/tools/vep/index.html doi: https://doi.org/10.1186/s13059-016-0974-4
Morgan AP, Fu CP, Kao CY, Welsh CE, Didion JP, Yadgary L, Hyacinth L, Ferris MT, Bell TA, Miller DR, Giusti-Rodriguez P, Nonneman RJ, Cook KD, Whitmire JK, Gralinski LE, Keller M, Attie AD, Churchill GA, Petkov P, Sullivan PF, Brennan JR, McMillan L, Pardo-Manuel de Villena F. The Mouse Universal Genotyping Array: From Substrains to Subspecies. G3 (Bethesda). 2015 Dec 18;6(2):263-79. doi: 10.1534/g3.115.022087.
Sarsani VK, Ashbrook DG, Beichman AC, Lu L, Palmer AA, Williams RW, Pritchard JK, Harris K. A natural mutator allele shapes mutation spectrum variation in mice, Nature, 605, 497-502, 11 May 2022. https://doi.org/10.1038/s41586-022-04701-5
Sarsani VK, Raghupathy N, Fiddes IT, Armstrong J, Thibaud-Nissen F, Zinder O, Bolisetty M, Howe K, Hinerfeld D, Ruan X, Rowe L, Barter M, Ananda G, Paten B, Weinstock GM, Churchill GA, Wiles MV, Schneider VA, Srivastava A, Reinholdt LG, The Genome of C57BL/6J “Eve”, the Mother of the Laboratory Mouse Genome Reference Strain, G3 Genes|Genomes|Genetics, Volume 9, Issue 6, 1 June 2019, Pages 1795–1805.
Srivastava A, Morgan AP, Najarian ML, Sarsani VK, Sigmon JS, Shorter JR, Kashfeen A, McMullan RC, Williams LH, Giusti-Rodríguez P, Ferris MT, Sullivan P, Hock P, Miller DR, Bell TA, McMillan L, Churchill GA, de Villena FP. Genomes of the Mouse Collaborative Cross. Genetics. 2017 Jun; 206(2):537-556. doi: 10.1534/genetics.116.198838.
Tretyakov, K. (2013). PyLiftover (0.4) [Python library]. https://github.com/konstantint/pyliftover
Yang H, Wang JR, Didion JP, Buus RJ, Bell TA, Welsh CE, Bonhomme F, Yu AH, Nachman MW, Pialek J, Tucker P, Boursot P, McMillan L, Churchill GA, de Villena FP. Subspecific origin and haplotype diversity in the laboratory mouse. Nat Genet. 2011 May 29;43(7):648-55. doi: 10.1038/ng.847.