Fig. 4.

The CC Viewer allows comparative analysis and visualization of multiple collinear genomes (Wang et al. 2012b) and follows the conventions reported previously (Collaborative Cross Consortium 2012; Yang et al. 2011). On the left side is a screenshot of the CC Viewer web site showing the fields for selection of the genomic region (chromosome, start and end), type, and identity of CC line(s) to be viewed. Note that in addition to the distributable lines, active lines, and CC founders, the browser has data for the entire CC population reported previously (Collaborative Cross Consortium 2012). On the right side of the figure is the output for four of the seven possible tracks for three distributable lines for chromosome 14. Data underlying the “Founder Mosaic” and “Subspecific Origin” tracks can be downloaded by clicking the appropriate blue tab. The phylogenetic tree for a specific region can be selected by clicking on the appropriate chromosome location in the “Haplotype Count” track. Users can zoom in by selecting a region in any of the tracks or by using the zoom tab. Clicking also allows centering the view on a given region and sorting according to the type of data shown in that track