TABLE B1

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
550.2460.6960.5550.6118.9175.0972.8420.994
10100.3240.8280.6090.58012.59011.1401.7690.829
20200.3680.7920.6710.59019.25021.6501.2740.770
40400.4680.8740.6380.51234.88043.4900.9360.591
80800.4600.8400.6910.49059.82092.5200.7660.624
1001000.5180.8200.6650.46277.190115.040.7270.604
Summary statistics method: acceptance rate = 15%
550.2650.6470.5470.40812.18739.77064.6194.024
10100.3980.7660.5890.52014.710213.46112.0751.590
20200.4830.8160.5940.57223.178521.9571.2820.771
40400.5880.8680.4760.46248.4444.901.0460.639
80800.5760.8500.4880.47991.5490.080.8430.581
1001000.6480.8520.4800.472109.68112.820.7420.563
Summary statistics method: acceptance rate = 30%
550.2420.7460.5740.3947.7685.7352.4020.914
10100.3580.8420.5330.58814.23010.5431.7520.694
20200.5220.8420.5800.60122.71720.8101.2150.662
40400.6380.8880.5430.49843.06043.5400.9370.567
80800.6040.8600.5140.53489.06086.6400.8390.562
1001000.6520.8460.4840.491109.58109.320.7430.554
Summary statistics method: acceptance rate = 60%
550.2330.7830.5650.4636.9134.8562.0200.754
10100.4070.8320.5680.65612.4469.6551.5140.631
20200.5550.8230.5710.67323.04318.8741.1970.558
40400.6540.9080.5670.59339.6639.100.8580.496
80800.6340.87205620.62380.1479.120.7390.520
1001000.680.8220.5700.55698.66101.740.6900.539