Fig. 4

Nucleotide-level associations between HIV-1 subtype and first-line treatment failures in HIV-1 A/D recombinants (n = 302). Each circle represents the result of a Fisher’s exact test at a specific nucleotide position in the HIV-1 pol reference sequence (x-axis). The locations of resistance-associated sites (triangles) within HIV-1 protease (PR) and reverse transcriptase (RT) are indicated at the bottom of the plot region. The area of circles were scaled in proportion to the sample size (range n = 79–302) at the respective nucleotide site, due to the varying coverage of partial sequences. Circles were coloured with respect to the P-value of each test (see inset legend). To avoid cluttering the plot, we thinned the number of tests to regular intervals of four nucleotides