During an entire lifetime, somatic mutations occur in DNA, which are the causes of many disease including cancer, complex diseases and probably ageing. While somatic mutations in genomic DNA have been widely analyzed from whole-genome or whole-exome sequencing, those that occur in mitochondrial genome have been rarely assessed due to the technical difficulties. As mitochondrial genome encodes many protein coding genes for energy metabolism and electron transport chain, mutations in mitochondrial genome and its resulting breakdown of genes may be associated or causative of related diseases. In this project we will develop a robust algorithm to assess somatic mutations in mitochondrial genome and use it for its clinical value for detecting, diagnosing or preventing human diseases.