Fig. 6

Results from the model A f₄(Chimpanzee, Human Reference Genome; Ind1_LINEAR, Ind1_MASKED/Ind1_GRAPH), B f₄(Chimpanzee, Human Reference Genome; Ind1_MASKED, Ind1_GRAPH) for both PMD correction strategies, and C f₄(Chimpanzee, Human Reference Genome; Ind1_Mapping_Strategy1_TRIMMING, Ind1_Mapping_Strategy1_REFINING) for all mapping strategies by using ancient genomes that FASTQ files available. The chimpanzee is the outgroup, and we are testing whether the Human Reference Genome is equally distant to the genetic data from the same individual but processed using alternative strategies (e.g., Ind1_LINEAR versus Ind1_MASKED). f₄ distributions shifted to the left or right suggest the reference genome shares more alleles with the genetic data processed using the methods indicated in the left or right, respectively. The color gradient from blue to red represents the fraction of comparisons that are nominally significant (|Z|> 3). See also Additional file 1: Fig. S34 for results when the genomes with just BAM files available are used