Fig 2. True binary data, observed binary data and binary mutation process example.

(A) True binary mutation matrix of the sequenced tumor cells in the mutation tree in Fig 1E. Each row represents true genotypes for one genomic site in all cells and each column represents the true genotypes of multiple genomic sites for one single cell. (B) Observed mutation matrix with missing and ambiguous values (red), as well as mutation states that are misrecorded with respect to the true mutation matrix (red numbers; these are either false positives or false negatives). The red dash indicates a missing value since the sequencing process does not return signal at this site of this cell, and the red question mark represents an ambiguous value. Each row represents observed states for one genomic site in all cells and each column represents the observed states of multiple genomic sites for one single cell. (C) Binary mutation process example. A mutation is acquired on branch e₁ (highlighted in red). The cell descending from branch e₈ (highlighted in black) does not carry the mutation, while the cells descending from the blue branches carry the mutation.