Common deletion breakpoints contain direct repeats and 2G QFP sequences. A) The "common deletion" breakpoints contain overlapping 2G QFP sequences. Boxes indicate the 13 nt direct repeats that comprise the breakpoint junction between ATP6 and ND5 in the common deletion. Direct repeat and flanking sequences in ATP6 and ND5 contain three overlapping QFP sequences. The N1b mtDNA sequence variant is 8472C > T. B) The highest frequency breakpoint is a 3’ breakpoint at 16071, which is right in the middle of a 2G QFP sequence. This region contains two different 12 nt direct repeat sequences, starting at 15990 or 16073. The cognate sites start at 1889 and 8637, respectively. Deletions involving 1889 or 8637 with the 16071 region are present in the deletion collection; however, there are approximately 200 unique deletions involving the 16071 region as the 3’ breakpoint for many other 5’ breakpoints .