Fig. 2: Mixed haplotype patterns and NUMTs observed in two families.

a Examples of the mixed haplotype patterns showing Family 2 and Family 6. Father and both offspring show the mixed haplotypes with the similar HFs in each family. The mixed haplotype patterns observed in the other five families are shown in Supplementary Fig. 2. b Screenshots from Integrative Genomics Viewer (IGV) showing aligned reads corresponding to the rare NUMTs. The alignment of the discordant and split reads corresponding to the NUMTs on the nuclear DNA (left) and mtDNA (right) in two families. Teal bars indicate the aligned reads which mapped to the nuclear DNA where their mates mapped to the mtDNA (left). The chromosomes on which their mates are found are shown in different colours (right). The genome position, repeats and segmental duplications tracks from UCSC genome browser are shown at the bottom. IGV Screenshots from all aligned reads corresponding to the rare NUMTs on the nuclear DNA are shown in Supplementary Fig. 3. IGV screenshots of the other five families are shown in Supplementary Fig. 4. c Circos plots show the observed variants and NUMTs in two families. Circles from the outside to the inside indicate the following: (1) position of a variant on the mtDNA; (2) regions corresponding to the different mtDNA genes; (3) variants identified in the mother where the radial axis corresponds to the VAF; (4) variants identified in the father; (5) variants identified in the offspring, proband (left) and sibling (right) are shown, respectively; (6) NUMTs observed in the family, proband (left) and sibling (right) are shown, respectively.