Deep coverage of the mitochondrial genome allowed us to manually curate sequences for 163 samples (Supplementary Information). While variants that were fixed within an individual were consistent with the known phylogeny of the mitochondrial genome (Supplementary Fig. 5), we found a considerable amount of variation within individuals (heteroplasmy). For example, length heteroplasmy was detected in 79% of individuals compared with 52% using capillary sequencing21, largely in the control region (Supplementary Fig. 6a). Base substitution heteroplasmy was observed in 45% of samples, seven times higher than reported in the control region alone21, and was spread throughout the molecule (Supplementary Fig. 6b). The extent to which this heteroplasmy arose in cell culture remains unknown, but appears low (Supplementary Information).
