Intro

Mouse Genome Browser

The Mouse Genome Browser can be used to visualize genes and the SNPs discovered in this study of genome-wide DNA variation in 15 commonly used, genetically diverse strains of inbred laboratory mice. The reference genome is the C57BL/6J strain NCBI build 37 mouse sequence. In addition to the experimentally-derived genotypes for the original 15 strains, the imputed genotypes for 40 additional inbred mouse strains can also be accessed.

Choosing Regions to Navigate

There are several ways to choose a region of the mouse genome to navigate. The same searches are available when using the browser itself by using the "Search" box located near the top half of the page

By Chromosome

View the entire chromosome. Click to zoom in.
Chr01 Chr02 Chr03 Chr04 Chr05 Chr06 Chr07 Chr08 Chr09 Chr10 Chr11 Chr12 Chr13 Chr14 Chr15 Chr16 Chr17 Chr18 Chr19 ChrX ChrY ChrM

By Chromosome Region

Enter a specific chromosome, start and end position (i.e. Chr06:115897546..115904449). Note, Chromosome 1 to 9 are Chr01, Chr02, .. Chr09. Chromosome X and Y are ChrX and ChrY. The mitchondria is ChrM.

By NCBI Gene Name

Gene Name from NCBI Gene Database (i.e. Rho)

By NCBI Transcript Accession Number

NCBI Genbank Accession (i.e. NM_145383.1)

By Submission SNP Identifier (ss#)

NCBI Assay ID (ss#). This is the ID dbSNP assigns to a SNP at the time of submission. (i.e. 48059685)

By Reference Cluster Identifier (rs#)

dbSNP rsIDs are not yet available for many of the SNPs. A future release may allow searches for SNPs using dbSNP rsIDs.

Viewing Genotypes

The “Genotyped SNPs” track displays all SNPs identified in this project. Clicking on a SNP will show the genotypes for each mouse strain. To see the subset of SNPs that are polymorphic within a subset of strains, use the “Reports & Analysis” drop-down menu to select strains of interest, then click Configure: the resultant SNP subset can be viewed in the “Genotyped SNPs Subset” track.

The genome browser can only display information mapped to a chromosome in NCBI Mouse Build 37. Approximately 0.6% of the SNPs discovered by Perlegen either cannot be mapped to a unique position in the genome ("unmapped") or are on a contig that has not been assigned to a chromosome ("ChrUn"). These SNPs are only available from our data download page.

Viewing Haplotype Block Boundaries and Dendrograms

The Haplotype Block track shows the boundaries of each haplotype block and provides information on the phylogenetic relationships between strains in each haplotype block. To access the phylogenetic data, select “Filter Haplotype Blocks” in the “Reports & Analysis” drop-down menu, select at least three strains, click Configure, and then click on the haplotype block of interest. The phylogenetic information, created using a pairwise distance matrix algorithm, is represented in the following ways:

• As a distance matrix, showing the pairwise distances for each pair of selected strains. Note that the columns represent the strains in the same order as provided in the rows.

• As a tree in standard Newick format (using a modified command line version of the phylip neighbor program).

• As a publication-quality image (using a modified command line version of the phylip drawgram program with DEFPLOTTER set to xbm, userxsize set to 3500.0 and userysize set to 3500.0).

Note that web browser Internet Explorer does not rescale these image files properly. Therefore, you may want to either user Firefox to display the images or save the images to your computer for further analysis.

The same phylogenetic data are provided at the chromosome and whole genome levels as well.