Figure 1.

Estimates of allele frequency at sites with a true MAF of 5% for different depths of coverage. At each depth, 1,000 sites were simulated using 200 individuals, and at each site, an estimate of allele frequency is computed using: (1) true genotypes (True); (2) called genotypes without filtering (Call NF); (3) called genotypes with filtering (Call F); and (4) the maximum likelihood method (ML). For more details of the estimation methods, see Methods.