Fig. 1

The human mtDNA reference map and the mtDNA deletion mapping pipeline. a Human mtDNA reference map, color-coded by feature. Inset: respiratory chain complexes encoded by mtDNA (color) and nuclear genes (gray). MtDNA-encoded genes and feature abbreviations: tRNA genes, IUPAC single-letter amino acid codes; rRNA genes, sedimentation coefficients (e.g., 16S); previously proposed heavy and light strand features, _H and _L; promoters, P_; replication origins, O_ (e.g., PH1, OL); and MT- prefixes are omitted. The 7S-3′-terminus and oriL are indicated (red and green arrows). b LostArc method outline. c The mtDNA fractions (mean ± 95% CL) indicate enrichment during library preparation and a subsequent lack of selection in sequencing (qPCR for steps 1, 3, and 4b, fraction of reads mapped to mtDNA reference for step 7). See also Additional file 1: Fig. S1. d Estimated mtDNA frequencies. Species with frequencies over 5 × 10⁻⁴ must reside in multiple truncated fibers (i.e., they predate adulthood or mark mutational hotspots). Deletions observed ≥ 2x must have ≥ 20 copies in the muscle sample. Deletions observed once will have frequencies inflated to roughly 1/depth. These collectively represent all less frequent species