Fig. 4: Recombination hotspots.

The ratio of various co-infection samples with sufficient evidence of a recombination breakpoint in different genomic positions. For this analysis, non-artificial co-infection samples were categorized based on their variant composition. Only those variant compositions are shown for which at least 10 samples were available in the raw read analysis pipeline. For each genomic position, the number of samples was calculated in which the given position is part of a recombination breakpoint range based on the evidence of at least 10 short reads and a recombinant read ratio of at least 0.1 of all reads overlapping the genomic position. Regions shaded with light red are recombination breakpoint ranges of the three Pango lineages (XF, XS, and XD) in which Delta – Omicron recombination occurs (see Supplementary Fig. 5). Areas shaded with light blue indicate intragenic hotspots.