Fig. 3

Size, position, frequency, and context of mtDNA deletions. a Frequencies of ≥ 20 bp deletions by Gwt age cohort and colored by degree of terminal microhomology (TMH; red to blue for 0 to 9 bp; green for ≥ 10 bp). TMH refers to identical sequences found in one deletion terminus and in the region flanking the other terminus. For simplicity, error bars (standard error) are only shown for 0, 5, and ≥ 10 bp of TMH. b–d Example visualizations of deletion frequencies by subsets of size, position, frequency, and sequence context (Gvar sample M24) with versions of the mtDNA map (b linear; c, d circular). The 7S-3′ terminus and oriL are indicated by red and green arrows. b A Bubble Map of deletions by terminal positions. Termini are classified starting from the center of a deletion (see inset diagram): one terminus lies in the light strand 5′-direction (red) and the other lies in the heavy strand 5′-direction (blue). Bubble area scaled by deletion frequency and colored by surrounding repeat tract (gray) or by the length of TMH: 0 bp (red); 1–9 bp (blue); ≥ 10 bp (green). The diagonal contains deletions of under 100 bp (peak in Fig. 2f). Minor and major arc deletions fall in the magenta and cyan areas (broad overlaid ranges of peaks in Fig. 2f). Plots equivalent to b may be found for all samples in Additional file 2: LostArc Reports (also see Additional file 1: Figs. S4 and S5). c An Arc Map with data as in b. Line width and transparency code for frequency (see deletion frequency key). Colors code for deletion size and terminal homology (see Length/homology key). Note the paucity of extensive TMH. The thin green arc from positions 8471 to 13,447 has been termed the common deletion. d As per c, but colors code for the degree of deletion terminus clustering (see Terminal Cluster key). Plots equivalent to c, d may be found for Gvar samples in Supplemental LostArc Arc Maps