We were recently interested in how many SNP sites would be generated by crossing the standard black 6 (C57BL/6J) laboratory mouse with any of the other mice that were genotyped by the Mouse Genome Project (MGP). To learn a little Javascript D3, I grabbed the number of SNPs for each strain (in 3 million basepair windows) and compared them to the standard C57BL/6J mouse. Below you can see a plot of the structure of these SNPs across the genome for each comparison strain. SPRETEiJ is by far the most divergent from C57BL/6J, which is expected (it's noted for this variation). Next came the CASTEiJ and PWKPhJ, good candidates if we'd like to generate a large amount of variation in the F1 progeny. A scale is located at the bottom. Also it's worth noting that the first and last bins are lacking variation. The first bin is usually mostly made up of N bases (something I don't control for), and the last bin is usually truncated in size (as well as having Ns). Also be a bit patient, the data may take a couple of seconds to load...