Extended Data Fig. 4: Mapping benchmark stratified by non-reference variants using RNA-seq data from NA12878.

Mapping error and recall for VG MPMAP and three other methods using simulated Illumina data. Colored numbers indicate different mapping quality thresholds. Reads are considered correctly mapped if one of their multi-alignments covers 90% of the true reference sequence alignment. Reads are stratified into those that a contain no variants, b contain no insertions or deletions (indels) and one single nucleotide variant (SNV), c contain no indels and two SNVs, d contain no indels and three SNVs, e contain no indels and more than three SNVs, and f contain any indels.