SOLiD reads were aligned to the B6 reference genome using two alignment tools: Corona Lite v4.0.2 (http://www.thermofisher.com/us/en/home/technical-resources/software-downloads/solid-software.html) and the MAQ code v0.7.1 (ref. 42). Corona Lite parameters were set to allow up to two and six mismatches for 25 and 50 bp sequence fragments, respectively. The longer reads from Illumina were mapped to the reference genome using MAQ, allowing up to two mismatches in the first 24 bp of each read. All alignment files were converted into BAM format. Reads that aligned to only one location with no more than two mismatches in the first 24 bp were considered uniquely aligned.
