TABLE 8

Estimating ρ in the presence of biased amplification

XNTpe = 0.01pe = 0.05pe = 0.1pe = 0.15
16×321.7 (7.8)21.9 (7.8)21.8 (7.6)21.7 (7.5)
521.9 (7.6)21.9 (7.7)21.7 (7.5)21.6 (7.5)
321.8 (7.6)22.4 (8.2)20.9 (7.6)21.2 (7.3)
521.7 (7.7)22.1 (7.6)22.1 (7.8)21.1 (7.2)
321.5 (7.7)21.6 (7.5)22.0 (7.8)21.1 (7.7)
521.0 (7.4)20.5 (7.1)21.0 (7.5)20.5 (7.2)
319.5 (6.7)20.1 (6.9)19.6 (6.6)19.5 (6.5)
513.4 (7.8)12.7 (8.22)12.5 (8.28)12.1 (8.8)
  • Here we set the generating values, θ0 = 100 and ρ0 = 20. NT is the number of reads required to use homozygous genotype calls in the inference and pe is the probability that a minor allele is not sequenced. We report mean (and RMSE) of the estimates over 1000 simulations.