Table 4 reports the percentage of Merlin recombinations that fall within a recombination region found by our method, and the percentage of our recombination regions that contain a Merlin recombination event. Percentages are given for each cohort separately. These results show only a rough concordance between Merlin and our method, with between 41% and 61% of Merlin recombinations detected by SHAPEIT2 and 80% to 89% of SHAPEIT2's recombination events concordant with Merlin. This table also shows the mean number of recombination events found by each method in maternal and paternal meioses. For comparison, the frequently cited deCODE 2002 genetic map estimated an average of 25.9 and 42.81 autosomal recombinations per paternal and maternal meioses respectively. The average number of recombinations for Merlin was substantially inflated across most cohorts (53 to 105 for maternal and 31 to 79 for paternal events) whilst SHAPEIT2's were in a more reasonable range (25 to 29 for paternal events and 41 to 47 for maternal events). Figure S25 plots the number of events found per meiosis by SHAPEIT2+duoHMM versus Merlin; there is obvious correlation but Merlin is typically reporting a much larger number of events than SHAPEIT2+duoHMM.
