(A) Mitochondrial pseudogene locations and chromosome gene densities. The diagram compares the location of mitochondrial pseudogenes with the known gene densities for chromosomes 1–22, X, Y, and the yet unassigned contigs (Un) of the human genome. The colored bars to the right side of the chromosomes mark the presence of mtDNA fragments that were integrated into the genome. Each bar shows a single integration event and can represent the integration of a single gene or a larger piece of mtDNA. The color of the bar is determined by the best homology that can be found within this fragment and is graded by the BLASTN score: >200 (red), 80–200 (blue), 50–79 (green), and <50 (gray).(Figure 2 continued on following page.) (B) Number of mtDNA integrations into the nucleus in relation to the degree of homology. The number of mtDNA integrations into the nucleus was calculated for each chromosome. In addition to isolated pseudogenes, every single pseudogene being part of a larger piece of integrated mtDNA was regarded as one hit. Depending on the degree of homology, the numbers were split into four groups following the grading that was used before (see Fig. 1). The height of each bar represents the sum of all unique pseudogenes on one chromosome. (C) Frequency of integration of mtDNA as a function of fragment size. The extent to which an integrated fragment covered the full-length mtDNA was calculated in percentage for each contiguous fragment of the map in Figure 1. The number of fragments covering a certain range of percentages was calculated and shown as five groups that are plotted separately for each chromosome.