Fig. 4: Overview of mtDNA variants detected by single-cell RNA sequencing.

a From top to bottom, mtDNA variants detected from single-cell RNA sequencing, cells defined as iPSC, mesendo and defendo stages are shown separately. Each dot represents the mean HF of each variant per cell line, and the error bar was 95% confidence interval; mtDNA variants observed in their fibroblast cells from bulk whole-genome sequencing (purple plot); mtDNA sequencing depth from single-cell RNA sequencing. Mean depth ± standard deviation (s.d.) is shown in the shaded area. Source data are provided as a Source Data file. b Overview of the variants detected in the single cells defined at iPSC, mesendo and defendo stages. The text labelled on mesendo stage also applies to the iPSC and defendo cell stages. c Distribution of the proportion of cells carrying the same variant from each cell line. The y axis shows the percentage of mtDNA variants. The majority of the variants were shared by a small proportion of cells from the same cell line. Cells defined as iPSCs, mesendo and defendo cells are shown in different colours. d Distribution of mean heteroplasmy fraction of each variant from each cell line. The y axis shows the percentage of mtDNA variants. The majority of the variants were low-level heteroplasmic variants (mean HF = sum HF/the number of cells carrying the same mutation). Cells defined as iPSCs, mesendo and defendo cells are shown in different colours. e Distribution of heteroplasmy fractions of pseudo-bulk variants from each cell line. The y axis shows the percentage of mtDNA variants. The majority of the variants were low-level heteroplasmic variants in pseudo-bulk heteroplasmy level (HF = sum HF / the total number of cells within each cell line). Cells defined as iPSCs, mesendo and defendo cells are shown in different colours.