Position of mtDNA deletion breakpoints relative to 2G QFP, 3G QFP, and direct repeat sequences. A) Circular plot of the mitochondrial genome specifying the location of deletion breakpoints and structural motifs. The center black lines connect the 5' and 3' breakpoints for each of the 730 deletions. The outer track depicts the mitochondrial genome with annotated tRNA (black), rRNA (brown) and protein-coding (green) genes. The control region is highlighted in gray. The inner tracks indicate the number of direct repeats (blue/white gradient), 3G QFP motifs (red/white gradient) and 2G QFP (green/white gradient), all measured in 100-nt windows. If a motif overlapped two 100-nt windows, it was considered to be in both windows. B) Schematic demonstration of the spatial arrangement of 3G QFP sequences and 3’ breakpoints for actual position (left) and a rotation-generated control (right). C) Schematic demonstrating a limited data set illustrating breakpoints (b-p) and rare motifs. Because breakpoints outnumber motifs, b-p to motif calculations are interpreted with caution due to assignment of multiple breakpoints to the same motif. Association using MDA can occur using b-p to motif or motif to b-p, but need not necessarily occur in both.