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Comparative study of DNA mutations occurring in human mitochondrial genomes in Indonesian humans and its comparison with some ethnic worlds has been done. The purpose of this study was to analyze mutant variants in all the complete human genome mitochondrial areas by using G-repliant techniques for mitochondrial genomic amplification, the result of Indonesian human nucleotide sequencing was then compared against some individuals representing some ethnicities in the world. DNA samples were isolated from human tissue and then sequenced using 10 pairs of primers to amplify human mtG. The mtG sequence is aligned and compared with rCRS using the DNAstar program. The result of mutation analysis shows the presence of point mutation in some mtG region fragments with different mutation proportions. Most mutations outside the HVS1 and HVS2 D-loops are in the ATP6 region. The encoding region of ATP6 is the gene coding region of human mtG and shows a high mutation rate of CRS. This opens a new paradigm for mutation analysis on ATP6 areas other than the mtG D-loop. The ATP6 gene segment located at 8553-8902 can be selected for studies in population genetics, forensic medicine and bioethnoanthropology studies, in addition to the HVS1/HVS2 D-loop areas that have been used.