CCGG

Collaborative Cross Graphical Genome

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Edge distribution
The brown curve on the top of the graph plots the average number of edges in every non-overlapping 10 kb windows over the entire 10 Mb region. The number of edges within a gap is weighted by the length of the reference edge.
The remaining eight curves plot the fraction of private edges for each founder strains. The corresponding founder strain for each plot is labeled on the y axis. The fraction of private edges for every founder is estimated based on the length of the private edges and the length of all edges with the corresponding founder haplotype in the window. For instance, the fraction of private edges for A is the length of all edges that are only shared by A divide by the total length of all edges that lie on the A path.
Founder strains on the clicked edge:


CCGG probe database

In the Founders column anchor nodes are shown as filled colored blocks. The colors match the strains shown as the first 8 read-count columns on the the right. An edge is depicted by a series of lines between each anchor indicating the founder strains sharing that edge. By clicking on an edge you can switch between alternate edges. The Position of each anchor is given in GRCm38.p6 coordinates while offsets from that anchor are provided for sequences on edges (Note, edge sequeces may overlap).


Normalized Colormap:   

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