Supplementary Figure 1: ROC curves as in main figure 2a for vg graphs with different allele frequency inclusion thresholds.
From: Variation graph toolkit improves read mapping by representing genetic variation in the reference
ROC curves parameterised by mapping quality for 10M read pairs simulated from NA24385 as mapped by bwa mem, vg to various 1000GP pangenome references, and vg with a linear reference, using single end (se) or paired end (pe) mapping. Allele frequency thresholds for the various rows are from top to bottom 0 (all variants), 0.001, 0.01, 0.1. Within each row, the left plot is based on all reads, middle on reads simulated from segments with no genetic variants from the linear reference, right on reads simulated from segments containing variants. All reads may contain simulated sequencing errors.
