Fig. 6

a Perfect/unique alignment results when aligning real reads. The blue curve is parametric, as a function of the fraction of variants included from 0% (bottom left) to 80% (top). The green diamond marks the number perfect and unique mappings for HISAT2’s custom variant pruning script applied to the set of SNVs and Indels. Graph genomes were built for SNVs alone (red) and for SNVs and Indels (blue), both ranked with the Pop Cov+ strategy. Blue and red diamonds mark the fractions that achieved the highest sum of unique and perfect alignments. b Allelic bias for the 2.07 M heterozygous SNVs that met a minimum coverage threshold of 25 in all experiments. Whiskers show the 5th-to-95th percentile range