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Expected values for genotype-call error rates (−log 10-scaled) under HWE for the Bayes classifier (BC) using true parameter values compared with MAQ using the true nucleotide-read error rate and MAQ's assumed heterozygote proportions of 0.2 and 0.001. Higher values on the -log10 scale correspond to lower error rates. We considered a nucleotide-read error rate of α = 0.01, read depths of N = 5, 10, 25, 50 and 100 and allele frequencies of p = 0.5 and 0.05.
