Table 2  Recombination rate estimates and the iHS statistic at the 16 largest known human inversions (≥500 kb)
Inversion location (chr: start–end in Mb)Inversion length (Mb)% of empirical dist. > max. ped/pop ratio% of empirical dist. < min. ped/pop ratio% of empirical dist. > max. abs(iHS)
8: 8.135–12.3694.2386.68.4639.5
8: 126.776–129.8033.0387.219.971.5
15: 28.524–30.6022.0821.417.21.91
9: 85.702–87.6411.9452.174.990.2
17: 16.659–18.2631.6085.311.89.40
17: 31.888–33.3931.5123.986.381.5
15: 72.151–73.3561.210.99188.780.1
8: 6.913–8.1031.191.16100100
16: 21.485–22.5951.112.672.3556.5
17: 40.900–41.9891.090.84744.686.8
13: 24.477–25.5421.0756.082.539.6
3: 12.128–12.8760.7560.640.038.5
4: 8.759–9.4620.700.10810037.7
16: 32.061–32.7430.6873.62.9858.0
16: 32.907–33.5390.631001.2778.3
13: 99.738–100.3120.5718.686.692.5
  • Pedigree-based and population-based (LDhat) recombination rate estimates from human genetic data are first compared by taking the ratio of the rates in 100-kb sliding windows genome-wide, as described in the text. Bias in these rates at inversion loci is investigated by computing the proportion of the empirical distribution that is greater and smaller, respectively, than the maximum and minimum “ped/pop ratios” observed within each of the 16 largest known human inversions (after omitting shorter inversions within, or overlapping, any of the 16 and any without markers between the breakpoints). The enrichment of values in the top 5% of the empirical maximum ped/pop distribution among the inversions has P = 0.000857 (5 of 16), and that in the top 1% has P = 0.000508 (3 of 16), assuming a binomial distribution, while the enrichment of values in the top 5% of the empirical minimum ped/pop distribution has P = 0.0429 (3 of 16) and there are no minimum ped/pop values in the top 1% of the empirical distribution at the inversion loci. Values of the iHS statistic were calculated genome-wide and investigated at the inversion loci similarly, with no enrichment of maximum absolute iHS values observed at the inversion loci (P = 0.560, 1 of 16 in the top 5% of the empirical distribution). dist., distribution; max., maximum; abs, absolute; ped/pop, pedigree/population.