How do I find genotyping polymorphisms between two strains?
Overview
You can use the Mouse SNP Query Form to search for mouse single nucleotide polymorphisms that are different between two strains. Use this form to search for SNPs by strain or strain comparison, dbSNP attributes, marker, marker range or associated gene.
Accessing the Mouse SNP Query Form
On most MGI pages, you can access the Mouse SNP Query Form from the Search menu as shown in the image at right.

For this tutorial, open the Mouse SNP Query Form in a new window. Scroll down this page for further instructions.

Search Menu SNP QF

Example 1. Finding SNPs that are different between A/J and BALB/cByJ
  1. Select A/J from the Available Strains window and click the Add button to move it into Selected Strains.
  2. Select BALB/cByJ from the Available Strains window and click the lower Add button to set this as the Reference Strain. The identity of the reference strain is arbitrary, but allows you to filter SNPs or display alleles as S (same) or D (different).

  3. Choose to return SNPs which are different between selected strains using the drop down menu.

  4. Enter map coordinates (GRCm38/mm10) or a marker range (use official gene symbols, rsID numbers are not supported) in the Map Position row. Select chromosome 1, then type 1-30 in the Genome Coordinates box and choose Mbp from the drop down menu.

  5. Select additional output options and specify whether output should be displayed on the web (as here), or downloaded. Strains which were fully sequenced as part of the Sanger Mouse Genomes Project will return many more SNPs than those which have genotype information only, and these files may take awhile to load, or be more manageable as downloaded Excel files.

  6. Click Search.
SNP QF Screen Shot
  1. SNP Query results will list all SNPs in dbSNP which meet the search criteria. This list can be downloaded, viewed in Mouse Genome Browser or a list of the Genes with matching SNPs can be generated.

  2. Click MGI SNP Detail to see more information including flanking regions of the SNP.

  3. The Function Class column will indicate if the SNP lies within a gene, and any functional notes that are attached to it (i.e. coding-nonsynonymous, intron, UTR).
SNP Search Results