The heteroplasmy at position 9309 is >2 kb away from the other heteroplasmies, which precluded identification of haplotype phase. By contrast, the heteroplasmies at positions 11755 and 12160 are ∼400 bp away from each other, which falls in the range of 454 sequencing read length, thereby enabling identification of haplotype phase. Consistently, we identified 35 reads covering both sites: 18 contained both reference alleles (11755G and 12160G) and 17 contained both alternate alleles (11755C and 12160A) (Figure S4).