ABI Bioscope software was used to align colour-space reads and to detect SNPs against the B6 reference genome. Similarly, MAQ software was used to align reads and to identify SNPs. A threshold of three or more supporting reads and a consensus quality score >30 (Illumina) and a confidence value >0.5 (SOLiD) was used to declare SNPs. Rare heterozygous calls, presumably generated by alignment errors, were discarded.
