Extended Data Fig. 1: Copy number and heteroplasmy estimation improvements using mtSwirl pipeline.

a. Overview of mtSwirl pipeline workflow. Colors represent genomic region analyzed (blue = chrM and NUMTs; yellow = chrM only); border style represents coordinate system (solid = GRCh38; dashed = self-reference coordinates). All output is in GRCh38. b. Percent change in mtCN estimated using ”vanilla” pipeline versus mtSwirl as a function of inferred nuclear ancestry. c. Percent change in mtCN among AFR individuals as a function of mtDNA haplogroup. d. Example of per-base coverage improvement with mtSwirl near a homoplasmic indel, likely due to use of mtDNA self-reference sequence. Arrows highlight homoplasmic indels. e. Example per-base coverage improvement likely due to reduced mis-mapping to nucDNA. Arrows highlight coverage improvements. f. Variant calls found using both pipelines (green), only in mtSwirl (red), and only in “vanilla” (blue). Inset corresponds to zoomed view of low heteroplasmy variants. g. 2D histogram showing relationship between heteroplasmy estimates using mtSwirl with ”vanilla”. Left panel corresponds to overall heteroplasmy space; middle is zoomed to low heteroplasmy variants; right is zoomed to high heteroplasmy variants.