Fluoroquinolone resistance mutations in ciprofloxacin-exposed bacterial communities. Total mutation frequencies quantified using Mumame for three known mutations conferring resistance to fluoroquinolone in the E. coli gyrA gene based on amplicon sequencing (A) and shotgun metagenomic data (B) from the same samples. Corresponding data for the S80 mutation in parC is shown in (C) for amplicon data, and (D) for shotgun data.