Extended Data Fig. 3: Comparative analysis of ReDeeM, mtscATAC, and MAESTER.

a, Comparison of the design and features of ReDeeM, mtscATAC and MAESTER to highlight their similarities and differences. b-d, Comparative analysis of before (as mtscATAC or DOGMA-seq) and after mtDNA enrichment (as ReDeeM), which is exemplified by young-1 HSPC dataset. b, Percentage of total reads mapped to mitochondrial genome per cell, before and after mtDNA enrichment. n = 14,808 cells. Boxplot displays data from the 25th to 75th percentile, and whiskers extending to the minimum and maximum within 1.5 IQR. c, Averaged mitochondrial genome coverage per cell at each position before and after mtDNA enrichment. d, Variant calling before enrichment using mgatk. 311 confident variants are identified. VMR: per mutation variance mean ratio. e-h, Comparative analysis of ReDeeM and MAESTER, which is exemplified by young-2 BMMC dataset. e, Mitochondrial genome coverage by MAESTER. f, mitochondrial genome coverage by ReDeeM. g, Mutational signatures of 307 top mutations by MAESTER, and 4087 variants by ReDeeM. n10 > 10: variants present in at least 10 cells with a VAF of >10%. h, Consistency between ReDeeM and MAESTER. n5 > 2: variants present in at least 5 cells with a VAF of >2%. See Supplementary Notes.