Collaborative Cross Viewer 2.0

Comparative genome browser for CC lines


We provide a tool to view and compare the haplotype structure among Collaborative Cross lines. The browser consists of three primary data sets:

      1. Founder mosaic - the inheritance mosaic of the eight CC founders
      2. Subspecific origin - the subspecific origin mosaic inferred from the computed subspecies of CC founders
         (Yang et al, 2011. Subspecific origin and haplotype diversity in the laboratory mouse.)
      3. Haplotypes - inferred haplotype structure (see ref)

In addition, we show the local phylogenetic structure of the eight CC founders. This can be seen by clicking anywhere in any other track.
Select a subset of available lines, genomic region, and click [View filter data] to get started. Navigation is described below.

Further details on the browser are explained in our paper (see reference).


Strain and genomic range selection


Build 37

3000000 = 3,000,000 = 3m = 3M = 3000k = 3KK

Start typing a gene name

Type a strain name to search. Multiple strains can be selected.
Click the box next to the set name to select all.

View filter data

To zoom in, click and drag across a track to highlight a region, then click [Zoom]



Jeremy Wang, Fernando Pardo-Manuel de Villena, and Leonard McMillan.
Comparative analysis and visualization of multiple collinear genomes. BMC Bioinformatics, 2012 13(Suppl 3):S13.

Collaborative Cross Consortium
The Genome Architecture of the Collaborative Cross Mouse Genetic Reference Population. Genetics, 2012 190:2 (389-401)