Reproducibility over time by sequence prevalence for a non-homogenous clinical sample (N = 47 replicates over 18 deep sequencing runs).

<p>A) The proportion of non-R5 virus (defined as PSSM≥−4.75) measured by sequencing run. Sequences in the “forward” direction are shown in black. Sequences in the “reverse” direction are shown in grey. Thick lines represent the overall mean percentage non-R5 virus measured from all sequences for that run. B) The number of times the 10 most common unique sequences were observed for the non-homogenous clinical sample are plotted against the sequencing run. Each sequence has a unique shade-shape combination.