Fig 1.
Analysis pipeline to identify mtDNA variants includes aligning sequence reads to the whole genome reference (including mtDNA rCRS reference); extracting mtDNA reads; combining mapped and unmapped reads to do a second alignment to the shifted rCRS reference; applying the mtDNA variant caller separately to the reads mapped to the two linear mtDNA reference genomes; and combining the two sets of called mtDNA variants.
Fig 2.
Sharing of mtDNA variants among 2,077 SardiNIA sequencing project participants.
Fig 3.
Two classes of base changes for homoplasmies and heteroplasmies.
Fig 4.
Distribution of homoplasmies and heteroplasmies in four functional categories.
Fig 5.
The effect of age on the number of heteroplasmies in the unrelated SardiNIA sequencing project participants.
The number of heteroplasmies increases with age with different (colored) minor allele fraction (MAF) thresholds. Each line plots the expected number of heteroplasmies based on the Poisson loglinear model against age at an MAF threshold; while the points represent the observed mean number of heteroplasmies in each age group (<40, 40–50, 50–60, 60–70, 70–80, >80).
Table 1.
The sharing of mtDNA variants in parent-child trios.
Table 2.
The effect of mtDNA copy number on a set of anthropometric, frailty, and lipid traits.