Estimation of population crossing-over and gene conversion rates
A. Whole LHB/CGB region | B. Recombination hotspot | ||||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Estonians | Han | Mandenka | Estonians | ||||||||||||
| All SNPs | ≥10% MAFd | All SNPs | ≥10% MAF | All SNPs | ≥10% MAF | All SNPs | >10% MAF | ||||||||
| Maximum PAC likelihood estimates (Li and Stephens 2003) | |||||||||||||||
| ρa (× 104) | 4.16 | 4.43 | 2.91 | 2.34 | 17.00 | 8.93 | 43.21 | 35.91 | |||||||
| Composite likelihood estimates (Frisse et al. 2001; Hudson 2001) | |||||||||||||||
| L = 0b | ρ (× 104) | 8.02 | 7.40 | 7.21 | 7.06 | 17.63 | 14.92 | 93.42 | 68.05 | ||||||
| L = 30 | ρ (× 104) | 6.38 | 6.25 | 6.60 | 6.53 | 12.29 | 10.38 | 68.05 | 56.17 | ||||||
| fc | 14 | 12.5 | 6 | 6 | 13 | 16 | 3 | 2 | |||||||
| L = 50 | ρ (× 104) | 6.36 | 6.21 | 6.55 | 6.53 | 12.29 | 10.32 | 67.36 | 54.63 | ||||||
| f | 9 | 8 | 4 | 3.5 | 8 | 10 | 2 | 1.5 | |||||||
| L = 100 | ρ (× 104) | 6.41 | 6.23 | 6.55 | 6.49 | 12.12 | 10.17 | 57.96 | 52.83 | ||||||
| f | 4.5 | 4 | 2 | 2 | 4.5 | 5.5 | 2 | 1 | |||||||
| L = 250 | ρ (× 104) | 6.41 | 6.13 | 6.82 | 6.68 | 12.18 | 10.11 | 35.96 | 34.58 | ||||||
| f | 2 | 0.5 | 0.5 | 2.5 | 2 | 2.5 | 3 | 2 | |||||||
| L = 500 | ρ (× 104) | 6.49 | 6.20 | 6.49 | 6.42 | 11.80 | 10.25 | 16.11 | 17.74 | ||||||
| f | 1 | 1 | 0.5 | 0.5 | 1 | 1.5 | 6.5 | 4 | |||||||
a The population crossing-over rate per base pair, ρ = 4Necbp.
b L is the length of the gene conversion tract.
c f = g/c is the ratio of gene conversion to the crossing-over rate.
d SNPs with minor allele frequency ≥ 10%.