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.
[List data sets]
• 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 Gbrowse
• 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
Deprecated SNP functionality and archived data sets.