Fig 5. Comparison of different post-mapping filtering strategies for high coverage bam files from anatomically modern humans employing mapping and base quality filters of 30.

(A) Average proportion of the alternative allele for the comparison between no additional filters (see also Fig 1), remapping of reads carrying the reference allele modified to carry the alternative allele (modified reads), remapping against a modified reference carrying a third allele at the SNP sites, and both filters together. (B) Influence of filtering on measures of heterozygosity for different fragment sizes in sf12. Error bars indicate two standard errors.