The genome of DBA/2J strain has recently been sequenced by our group with 100 × average coverage using Illumina GAII and ABI SOLiD technologies.39 Reads with 25 and 50 bp from SOLiD and reads with 100 bp from Illumina GAII and HiSeq 2000 were mapped to the C57BL/6J reference genome using Corona-Lite v 4.0.2 (http://solidsoftwaretools.com/gf/) and the MAQ program v0.7.1,40 respectively. A threshold of three or more supporting reads and a consensus quality score >30 (Illumina) or a confidence value >0.5 (SOLiD) was used to declare SNPs. A complete compendium of new polymorphisms between the D2 and B6 (the source of the reference mouse genome) parental strains are freely available at GeneNetwork (www.genenetwork.org), and original sequence data are available at www.ncbi.nih.gov/sra.
