Application of dataset filtering steps to the public datasets (Supplementary Table S2). (A) Number of SNVs detected using LoFreq grouped by patient after each step. The colour of each point indicates the patient, and the shape indicates whether the dataset represented a single-strain (dot) or a multiple-strain (star) infection. (B) Violin plots showing the distribution of the number of reads identifying the SNVs detected using LoFreq for each dataset. The number of supporting reads was truncated to 25 when >20.