Transitions and may correspond to crossover events or SEs in the parental haplotypes. The 2002 deCODE map gives the chromosome 10 genetic length as 1.34 and 2.18 Morgans for males and females respectively [37]. The mean numbers of or transitions in the SHAPEIT2 show rough agreement with the expected number of recombinations on chromosome 10 in most cohorts. For example, in the VIS cohort we observe and transitions in males and females respectively. The female rates in CARL are higher than we might expect at 2.8. Both the male and female rates are lower than we might expect in the Korcula and Split cohort. This is likely due to insufficient information in the data to infer the true parental haplotype and hence we are seeing a parental SE at the recombination event, that is, we are inferring the transmitted haplotypes.
