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
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)