Fig. 1

Deep mutational scanning and Enrich2. In a deep mutational scan, a library of protein variants is subjected to selection, which perturbs the frequency of variants. Samples of the library are collected before, during, and after selection and subjected to high-throughput sequencing (left panel). Enrich2 processes the high-throughput sequencing files generated from each sample. Sequencing reads are quality filtered and variants are counted by comparing each read to the wild-type sequence. Enrich2 estimates variant scores and standard errors using the variant counts and combines these estimates for replicates (middle panel). Enrich2 displays the scores and standard errors as a sequence-function map. A sequence-function map of eight positions of the hYAP65 WW domain is shown (right panel). Cell color indicates the score for the single amino acid change (row) at the given position in the mutagenized region (column). Positive scores (in red) indicate better than wild-type performance in the assay and negative scores (in blue) indicate worse than wild-type performance. Diagonal lines in each cell represent the standard error for the score and are scaled such that the highest standard error on the plot covers the entire diagonal. Standard errors that are less than 2% of this maximum value are not plotted. Cells containing circles have the wild-type amino acid at that position. Gray squares denote amino acid changes that were not measured in the assay