Preference

Growth/Fitness

Preference

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Illumina Sequencing , Deep Mutational Scanning , Growth Selection , PCR

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For details please refer to doi: 10.1093/molbev/msu173 or http://jbloom.github.io/mapmuts/example_2013Analysis_Influenza_NP_Aichi68.html

Briefly, we use the DNA amplicons to estimate the sequencing error rate that afflicts the mutDNA amplicons, and the RNA amplicons to estimate the sequence / reverse-transcription error rate that afflicts the mutvirus-p1 amplicons. We then infer the preferences based on changes in frequency going from the mutDNA to the mutvirus-p1 (which involves selection for viral growth).

We infer the preferences separately for each replicate, averaging over all of the samples for the replicate. We then compare the inferred preferences among the replicates, and summarize the results graphically.