Figure 2.

Coverage plots normalized to within-sample median (see text), used to illustrate the uniformity of coverage across each amplicon and compartment. Solid lines are median values computed over all 14 individuals, and grey areas show the 2.5–97.5 percentile range. Systematic dips in env coverage coincide with the region AAGAAAAA, where length miscalls of the A homopolymer are repaired by codon-aware alignment and partial codons (e.g. –AA) are not counted toward position coverage. In RT, the dip in coverage corresponds to a similar homopolymer context (AAAAAAGAAAAAA).