TABLE 5

Performance for models with nonuniform crossing over and uniform gene conversion 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
20200.4200.9720.7800.50912.49920.3200.9860.448
60200.5920.9580.7630.41339.47922.3900.6680.533
80200.6360.9480.7760.41859.15922.1020.6110.535
20400.2880.9640.8410.6549.44037.0001.0470.360
40400.3840.9840.8530.57818.94039.7200.8560.356
Summary statistics method
20200.5780.9380.5010.52824.48221.2201.2080.598
60200.7320.8660.5290.49866.33022.5780.7450.773
80200.7720.8320.5180.48684.51824.4120.6000.911
20400.4580.8940.5490.69525.31236.0301.4620.457
40400.6080.880.5610.62342.80038.4640.9740.503
  • 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.