Mitochondrial DNA heteroplasmic variants can be detected in MPS data down to a frequency of 2%, although they can be confused with NUMTs. It’s especially a problem when there is more noise in MPS data, as it's harder to distinguish between minor variants and NUMT sequences. 

This study used qPCR methods to assess the ratio of mtDNA to nDNA to explain noise observed in MPS data within buccal versus blood samples, collected with varying methods.