Mouse Haplotype Browser Help
Haplotype blocks of 16 inbred mouse strains (including wild-derived strains) were predicted by merging the results of pairwise comparisons of the mouse strains. The pairwise scores were determined by using a Hidden Markov Model (HMM) trained to detect low-SNP-density and high-SNP-density regions. Haplotype block regions are detected when the matching HMM changes state from low-density to high-density or vice-versa. The sequences of 16 commonly used, genetically diverse strains of inbred laboratory mice were analyzed to determine their haplotype structure. The Ancestry Browser shows which ancestral sequence each inbred strain most resembles, along with statistics on the pairwise similarity between the ancestral strains. The Haplotype Viewer shows the haplotype block boundaries and the pairwise similarity for all 56 strains: the 15 used for SNP discovery, the reference strain (C57BL/6J), and the 40 additional strains for which the genotypes were imputed .
Main Display
In the visualization, a haplotype block will be colored either with a preceeding strain's color, if it matches, or its own strain color otherwise. Areas that are grey lack information. Sequence coordinates are provided at the bottom of the display.
Chromosomal Location
The current chromosome and sequence position is shown in the text box at the top of the display.
To change the current location, enter the sequence location in the format "chr[#]:[start]..[end]" and click submit.
(The format "Chr[#]:[start]-[end]" is also allowed.)
Similarity Coloring
In this visualization, the ordering of the strains is important. Each strain is colored by the preceeding
strain in the list which has the highest similarity score. If no match exists, then the strain is rendered in its own color.
You can change the ordering of the strain comparisons with this control. The strain in yellow is always the most
significant, followed by red, green, blue, etc. The strain in peach is always the last comparison.
Navigation
Clicking on the main ancestry display will center and zoom on your position by default.
You can also zoom in or out by clicking on the zoom bar. You can scroll by clicking on the arrow bar on either
side of the viewer.
Haplotype Density
The number of distinct haplotypes for each block is shown in this section.
Other Commands
The bottom button shows genes, transcripts, ESTs, and other information for the current region from the UCSC site.