Distribution of natural variations at 500 gag positions of HIV-1 group M (subtypes: A1, B, C, D, F1, G and CRF01_AE, CRF02_AG). The first position of each protein region is labeled with its protein name in a box. Annotated protein regions are indicated as colored bars: light-green for matrix (positions 1–132), light-blue for capsid (133–363), dark-green for p2 (364–377) and p1 (433–448), dark-blue for nucleocapsid (378–432) and grey for p6 (449–500). HXB2 indices for both full-length gag and individual proteins are shown on top of the colored bars (e.g. '180|48’ indicates the gag position 180 and the capsid position 48). Known drug binding positions are marked with red stars. Consensus subtype B amino acid for each position is shown directly under the bar, and is highlighted green when the consensus AA differed in one or more subtypes. Natural polymorphisms are shown below the consensus subtype B amino acids; proportions (%) are colored blue for proportion ≥ 5%; orange otherwise. Figure S1 in Additional file 2 provides the distribution of natural polymorphisms within each individual subtype.