TABLE 6

Conditional probabilities of haplotype configurations and summary statistics for s = 10 and n = 7, obtained from simulations

Configuration
 (c)q(c|s, n, θ)Cumulative
 probabilityℙ[MM(c)]ℙ[MM(c)]ℙ[KK(c)]ℙ[KK(c)]ℙ[HH(c)]ℙ[HH(c)]
Bayesian approach with a prior of θ ∼ unif[0, 20] (procedure 3)
(7, 0, 0, 0, 0, 0, 0)0.04370.17641.00000.04371.00000.04371.00000.0437
(5, 1, 0, 0, 0, 0, 0)0.22971.00000.95630.53060.95630.27340.95630.2734
(3, 2, 0, 0, 0, 0, 0)0.21980.77030.95630.53060.72660.64050.72660.4932
(1, 3, 0, 0, 0, 0, 0)0.03740.13270.95630.53060.35950.90470.50680.6779
(4, 0, 1, 0, 0, 0, 0)0.14730.39580.46940.86290.72660.64050.50680.6779
(2, 1, 1, 0, 0, 0, 0)0.15470.55050.46940.86290.35950.90470.32210.8326
(0, 2, 1, 0, 0, 0, 0)0.01440.02440.46940.86290.09530.99000.16740.8470
(1, 0, 2, 0, 0, 0, 0)0.01590.04030.46940.86290.09530.99000.15300.9350
(3, 0, 0, 1, 0, 0, 0)0.07210.24850.13710.96960.35950.90470.15300.9350
(1, 1, 0, 1, 0, 0, 0)0.03190.09530.13710.96960.09530.99000.06500.9669
(0, 0, 1, 1, 0, 0, 0)0.00270.00530.13710.96960.01001.00000.03310.9696
(2, 0, 0, 0, 1, 0, 0)0.02310.06340.03040.99530.09530.99000.03040.9927
(0, 1, 0, 0, 1, 0, 0)0.00260.00260.03040.99530.01001.00000.00730.9953
(1, 0, 0, 0, 0, 1, 0)0.00470.01000.00471.00000.01001.00000.00471.0000
Fixed-S approach (Hudson et al. 1994)
(7, 0, 0, 0, 0, 0, 0)0.03730.12161.00000.03731.00000.03731.00000.0373
(5, 1, 0, 0, 0, 0, 0)0.19510.78890.96270.48520.96270.23240.96270.2324
(3, 2, 0, 0, 0, 0, 0)0.21121.00000.96270.48520.76760.58380.76760.4435
(1, 3, 0, 0, 0, 0, 0)0.04170.16330.96270.48520.41620.87330.55650.6254
(4, 0, 1, 0, 0, 0, 0)0.14020.42570.51480.82920.76760.58380.55650.6254
(2, 1, 1, 0, 0, 0, 0)0.16800.59380.51480.82920.41620.87330.37460.7935
(0, 2, 1, 0, 0, 0, 0)0.01590.03220.51480.82920.12670.98370.20650.8094
(1, 0, 2, 0, 0, 0, 0)0.01980.05200.51480.82920.12670.98370.19060.9090
(3, 0, 0, 1, 0, 0, 0)0.07980.28550.17080.95570.41620.87330.19060.9090
(1, 1, 0, 1, 0, 0, 0)0.04240.20570.17080.95570.12670.98370.09100.9514
(0, 0, 1, 1, 0, 0, 0)0.00430.00430.17080.95570.01631.00000.04860.9557
(2, 0, 0, 0, 1, 0, 0)0.03230.08430.04430.99330.12670.98370.04430.9879
(0, 1, 0, 0, 1, 0, 0)0.00530.00960.04430.99330.01631.00000.01210.9933
(1, 0, 0, 0, 0, 1, 0)0.00670.01630.00671.00000.01631.00000.00671.0000
  • Cumulative probability refers to the sum of the probabilities of all configurations that have probability at most q(c|s, n, θ). For the Bayesian approach, empirical probabilities are based on 10,000 accepted genealogies; for the fixed-S approach, empirical probabilities are based on 10,000 genealogies.