TABLE 4

Comparison between haplotype and genotype data: performance for models with uniform recombination rates with phased 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
20200.3820.9160.6690.55020.0620.861.3960.624
60200.6260.8900.5890.48151.5623.440.6720.765
80200.6720.8560.7170.43162.1925.360.6000.869
20400.3260.8900.6960.49618.9442.491.5570.519
40400.4400.8620.6860.49533.4843.000.9940.550
Summary statistics method
20200.6100.9440.4820.52326.4821.761.4270.635
60200.7400.9220.4780.53067.4621.740.7140.661
80200.8040.8940.5090.49283.1622.800.5660.717
20400.4400.9140.4890.56030.0640.061.7420.471
40400.6420.8920.5340.49843.5642.760.9290.510
  • 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.