The parents of the BXD cohort differ at 4.8 million single-nucleotide polymorphisms (SNPs) (Fig. 2c) at a high-confidence threshold, including 4,160,570 extracted from the SOLiD platform and 4,090,000 SNPs from Illumina (Supplementary Fig. 1a). Recently, Keane et al.4 generated ∼25-fold coverage of the D2 genome using the Illumina platform. We found a reasonably high concordance (94.4%) in SNP detection between Illumina data and that of Keane et al. (Supplementary Fig. 1b). The distribution of SNPs across functionally distinct genomic regions is provided in Supplementary Fig. 1c and Supplementary Note 1. We resequenced a subset of 262 platform-specific SNPs. False positive rates (FPR) were 2.34% and 3.73% for SOLiD and Illumina platforms, respectively. Assuming that all 3,375,198 SNPs detected by both systems are valid, the FPR are 0.44% for SOLiD and 0.65% for Illumina.
