Figure 6

Inferring Polymerase Errors from Misincorporation Counts. The conceptual relationship between mutagenic PCR, the unselected clone population, and characteristics of the Taq polymerase. The top-left depicts a wild-type sequence that, when subject to mutagenic PCR, results in a clonal population that has not been selected for functional integrity. The number of misincorporations from a wild-type nucleotide to a clone-type nucleotide is summarized as 'Observed PCR Misincorporation Counts' matrix C. The top-right depicts how relative Taq misincorporation rates are implicitly assumed from the 'Expected Polymerase Transition Matrix' T that describes how Taq incorporates nucleotides onto the nascent strand. These misincorporation probabilities are converted to 'Expected PCR Misincorporation Frequencies' P via nonlinear 'PCR Operator' Φ, described in the text, that models the multi-cycle PCR process. A Bayesian procedure is used to determine the compatibility of the given parameters with the observed data, as described under 'Methods'.