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Figure S1. Possible locations of the junction site in the presence of a perfect direct repeat (bold underlined nucleotides) at 5’ and 3’ breakpoints

Figure S2. Distribution of deletions and duplications breakpoints throughout the human mtDNA.

Figure S3. Two-dimensional scatterplots showing the location of the 730 mtDNA deletions (black dots) and 37 mtDNA duplications (red dots) in the seven groups.

Figure S4. Two-dimensional scatterplots showing the breakpoints of the 730 mtDNA deletions (A and B) and 37 duplications (C and D).

Figure S5. Distribution of 5’ and 3’ deletion (blue and red bars) and duplication (yellow and green bars) breakpoints in the human mtDNA. The frequency of missing sites (grey area) is defined as the number of times that each mtDNA L-strand position is missing in the 730 different mtDNA deletions.

Figure S6. The distribution of deletions (top graph) and duplications (bottom graph) is depicted for all combination of 500-nt windows from the mitochondrial genome.

Table S1. General features of mtDNA deletions and duplications

Table S2. Description of the seven mtDNA duplications exclusively located inside the control region

Table S3. Description of the seven mtDNA deletions and duplications with equal breakpoints

Table S4. Distribution of mtDNA deletions and duplications according to the length of the perfect direct repeat (DR) present at breakpoints

Table S5. List of all mtDNA deletions detected in four or more groups

Table S6. Length of perfect direct repeats (DR) present in all combinations of flanking regions of the 730 deletions and 37 duplications reported in human mtDNA

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