Figure 4

Variability of the number of G-to-A mutations within the endogenous IAPE-D and HERV-K proviruses depending on the element. The total numbers of G-to-A mutations (plain + hatched grey bars) for each IAPE-D (A) and HERV-K (B) proviruses are represented, together with that of the C-to-T (black bars) "none-strand-specific" mutations, given as an internal control (also used for ordering the elements) indicative of the genetic drift-associated age-dependent amount of mutations for each copy (same rank order as the sum of all non-G-to-A base substitutions). The number of G-to-A mutations specifically associated with the mA3 or hA3G APOBEC footprints is indicated with hatched grey. (C) Positioned G-to-A mutations (red bars) specifically associated with the hA3G APOBEC footprint ("GG") for the individual HERV-K elements in (B); yellow bars correspond to deletions in the proviruses (relative to the Phoenix consensus sequence). The data and the image shown in figure 4C were generated using the Hypermut 2.0 software available at the http://www.hiv.lanl.gov/ website.