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SNP / genotype variation

MPD has a number of mouse SNP and genotypic variation data sets that characterize the genotypes of mouse strains.


• SNP / variation query   Retrieve SNPs, indels, or SVs from one or more data sets using a step-by-step web interface. Variation data can be viewed as a table, as a polymorphism matrix, in a "Hap view" where strains are grouped by similarity of genotype, or downloaded as CSV files. [Query] [List data sets] [Documentation] [Downloads] [Query examples]


• Compare genotypes for two strains, or
• Retrieve genotype data for one strain

After selecting strains click Next then find the SNP/variation link towards the right side. See also Whole Genome Comparisons below.


• Find genes where certain strains are highly polymorphic
Select two strains, or sets of strains. This tool will list all genes where your strains are polymorphic to a specified degree, based on Sanger1 SNP data.



• Exporting and importing gene sets   to and from MPD


• Whole genome comparisons     Extractions done by MPD. [Caveats]
    • B6diff1: all sites where C57BL/6J differs vs. C57BL/6NJ in Sanger1
    • B6diff2: same as above but Sanger2 indels
    • 129diff1: all sites in Sanger1 where the 129 strains are polymorphic



• External genotype and variation resources
    • MGI        • MGI Gbrowse
    • CGD       • CGD SNPdb       • CGD mouse phylogeny viewer
    • UCLA mouse genotype resources
    • Sanger mouse genomes project     • Sanger web query
    • NCBI dbSNP       • NCBI dbVar
    • JAX exome data for 16 inbred strains (FASTQ files, Illumina)
    • Ensembl variation


• Archives   Deprecated SNP functionality and archived data sets.


 




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