FIG 1.

Distribution of MiSeq sequencing coverage. The depth of MiSeq sequencing coverage at each position across the sequenced amplicon (RT codons 90 to 234), after quality control filters were applied (n = 892 clinical samples), is shown. Red line, median coverage at each position; pink shading, interquartile range. Paired-end 2x250-bp sequencing kits were used. Arrows, positions covered by each read in the pair. The small drop in coverage observed around RT codon 170 reflects lower-quality bases at the end of read 2, which were discarded during data processing.