The phased MHC region has lower recombination rate than the genome-wide average while the density of typed SNPs is substantially higher than average. We applied the same phasing algorithm to a location on 15q25 where the recombination rate is approximately 1 cM/Mb and where we have about 90 typed SNPs per Mb, both close to the genome average. We considered two regions, one longer (~ 10.0 Mb, 895 SNPs) and one shorter (~ 6.4 Mb, 574 SNPs) (Supplementary Results online). For the longer region, the results matched the MHC closely; overall yield of 93.5% for the run with 35,528 individuals and a discrepancy rate of 0.080% in the trio test. Results for the shorter region were better; overall yield of 95.2% with a discrepancy rate of 0.022% (Table 2 and Supplementary Table 1a). For all three regions investigated, as part of the trio test with parents removed when applying LRP, we found that those offspring without siblings genotyped (1249 out of 2718) have yield that are approximately 1% to 2% lower than the overall, but there is little difference in the discrepancy rates (Supplementary Table 1b online).
