Site saturation mutagenesis uses primers with a degenerate codon to scramble a single residue. Quick-quality control (QQC) is a way to determine extent of randomisation by sequencing the pool of plasmids, measuring the peaks and calculating the deviation from an ideal mix (Acevedo-Rocha et al., 2015 ).
This tool performs automatically the peak measurements, Q-value calculations and expected amino acid proportions. In the case of sequences mutated with multiple codons a rough estimate of the contributions of each is obtained by optimining the function:
This approach therefore tries to balance the primers so to minimise the deviation from the ideal primer mix. The usage of the ideal primer mix is unfortunate, but is the only way to tackle the problem of deconvoluting the primers.