Reply to: Artefacts in single-cell mtDNA analyses misinform phylogenies

(a) Example mtDNA mutations that show lineage specificity. The 1+-molecule mutations are represented in triangles with colors. The mutations with more molecules per cell are represented in black dots. (b-d) Related to Fig. 1g,h. (b) Reanalysis of the agreement of closeness (AOC) between ReDeeM and CRISPR lineage inference using ReDeeM pipeline by cell-ranger (bwa) as aligner (without mitochondrial genome masking) is computed with or without edge trimming. (c) AOC distribution compared to random reshuffled for panel-b. (d) AOC distribution using all mtDNA mutations called by 4 varieties of ReDeeM pipelines, where two aligners: bowtie2, and cell-ranger (bwa) and two consensus calling thresholds are tested. (e-f) Extended example from a different tumor sample is shown, related to Fig. 1g,h, The agreement of closeness (AOC) between ReDeeM and CRISPR lineage inference is computed across ReDeeM filter1 and filter2. 4 panels are in the same order. The AOC is computed for (1) mtDNA mutations using filter1, including 1+-molecule mutations, (2) mtDNA mutations using filter1, excluding 1+-molecule mutations (3) mtDNA mutations using filter2, including 1+-molecule mutations (4) mtDNA mutations using filter2, excluding 1+-molecule mutations. The regions with enhanced AOC when including 1-molecule mutations are highlighted. AOC distribution across different mtDNA filtering strategies compared to random reshuffled is shown in panel f.