FIG 3.

Schematic of marker configurations and how to compare between them. (A) In this study, recombination is measured between wild-type virus and a marker system with silent codon modification markers that do not affect any viral proteins or packaging (marker configuration MK_high). To test that these codon modifications do not influence our recombination rate measurements, a second marker system virus is created where the codon modifications occur at different nucleotide positions (marker configuration MK_low). (B) To compare between marker configurations, MK_high is used to predict what would be measured as the recombination rate if MK_low was used. This prediction can then be directly compared to the experimental results for MK_low. For each interval in MK_low, the MK_high prediction is calculated by averaging the overlapping MK_high interval's recombination rate and weighting this average by the proportion of overlap.