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â¢ Mitochondrial DNA is found inside the mitochondria while nuclear DNA is found inside the nucleus of a cell. â¢ One cell contains approximately 99.75% of nuclear DNA and 0.25% of mitochondrial DNA.â¢ The mutation rate of mitochondrial DNA is nearly twenty times faster than that of nuclear DNA.he uniqueness of mitochondrial DNA is that it is maternally inherited as a linked set of genes, passed on to progeny in the cytoplasm of the egg cell; thus no recombination between maternal and paternal genomes occurs.
The main difference between nuclear DNA and mitochondrial DNA is, nuclear DNA is the standard 46 chromosome containing DNA in which you inherit 23 chromosome from one parent and the rest 23 from another one. On the other hand, mitochondrial DNA contains just one chromosome, like a circular genome.