Accurately Measuring Recombination between Closely Related HIV-1 Genomes
An optimal recombination rate is calculated by minimizing the chi-square value between the observed and expected frequencies of detectable template switches in each of the regions. A chi-square goodness of fit test indicates whether recombination rates are likely to vary over the entire length. (A) Variation between expected and observed frequencies (B) A dual recombination rate model was fitted and marker point 4 was the optimal location for a recombination rate switch. (C, D) In a second independent experiment we also observe that recombination is higher towards marker region 1 and lower towards marker region 6. However an F-test comparing a single recombination rate model (C) and a dual recombination rate model (D) with the switch location known from the original experiment, still did not achieve significance (p = 0.068, F-test).