Post date: Nov 23, 2015 5:45:9 AM
I redid the analysis from here, but with the 'inversion' or region of interest defined based on the HMM results.
If we define the region of interest as spanning any scaffold with one or more windows in the high HMM state in either population (N1 or FHA) and any scaffolds between these, we get 18-66 as the region of interest. I re-tested for elevated differences in recombination rate between parents for pairs of variants that cross the region of interest boundary vs. those that do not. Consistent with our other tests with slightly different regions, we find that recombination rates differ more between parents for pairs that cross the boundary:
obs = 0.0122, null = 3.28e-5, 95th quantile = 0.00665, p = 0.001