TABLE 3

Comparison between haplotype and genotype data: performance for models with uniform recombination rates with unphased data

γaρag(γ)bg(ρ)bB(γ)cB(ρ)cE(Embedded Image)dE(Embedded Image)dV(γ)eV(ρ)e
Hudson's composite-likelihood method
20200.4520.9680.6000.57322.06020.1701.2730.495
60200.6920.9540.5450.49155.25921.5940.6500.573
80200.7940.9620.6260.54374.11920.9080.5340.564
20400.4200.9680.6620.48419.91942.0001.3450.426
40400.5720.9600.6190.53436.62040.8800.8630.417
Summary statistics method
20200.5800.9100.4450.49827.60022.7001.3870.715
60200.7320.8500.4540.45370.27824.0900.7630.822
80200.7480.8380.4680.51489.94023.2260.6540.872
20400.4880.9040.5160.52128.07642.5821.6730.512
40400.6000.8280.5010.54151.81443.0501.1690.590
  • a γ and ρ denote the true values of the gene-conversion and crossing-over rates under which 500 data sets were simulated.

  • b g(γ) and g(ρ) denote the fraction of the data sets for which the estimates of gene conversion (Embedded Image) and crossing over (Embedded Image) lie within a factor of 2 of the true values (i.e., γ and ρ), respectively.

  • c B(γ) and B(ρ) denote the fraction of times the estimates of gene conversion and crossing over are lower than the true values, given that they are not equal to the true values.

  • d E(Embedded Image) and E(Embedded Image) denote the mean of the estimates of gene-conversion and crossing-over rates.

  • e V(γ) and V(ρ) denote the root mean square relative error for the estimates.