Distribution of the minor allele frequency estimated from the exomes of 200 sequenced individuals. For each site, the minor allele frequency was estimated using four different methods: (1) the ML method with unknown minor allele, (2) the ML method with a known or fixed minor allele, (3) calling genotypes without filtering (Call NF), and (4) calling genotypes with filtering (Call F). Each site is classified into bins based on the depth of coverage. Furthermore, in each histogram, sites with estimated MAF less than 2% are not considered. For the number of SNPs that were used for this analysis, see Table 1.
Kim et al. BMC Bioinformatics 2011 12:231 doi:10.1186/1471-2105-12-231