Figure 6 compares the distribution of the number of recombination events found by Merlin and our method to what we would expect according to the 2002 deCODE family based map. Figure 6 (top) plots the observed against expected number of recombinations in paternal and maternal meioses for each chromosome. The results from SHAPEIT2 are well calibrated against the expectation, whereas the Merlin haplotypes exhibit elevated levels of recombination. Figure 6 (bottom) shows QQ-plots comparing the observed and expected number of genome-wide recombinations in paternal and maternal meioses for each duo when using a Poisson distribution with rates 25.9 (paternal) and 42.81 (maternal) as our expected distribution. SHAPEIT2 rates are well calibrated against the expectation for paternal meioses, with some over-dispersion present in maternal meioses compared to the Poisson model. Figures S26, S27, S28, S29, S30, S31, S32 show these QQ-plots for each of the other cohorts separately.
