Supplementary Figure 7: Substitution matrices from alignments using expectation maximization–trained model.

Maximum-likelihood estimates and standard-error parameters for substitution matrices show trends across template, complement and 2D reads across three M13 experiments using R7.3 chemistry. The top row illustrates the average maximum-likelihood estimates for these substitutions, with the standard error represented in the lower row. For all aligners, thymine-to-adenosine and adenosine-to-thymine substitution rates were low, indicating that the device rarely miscalled one as the other. The color scheme is fitted on a log scale, and the substitution values are on an absolute scale.