Fig. 2.

Recombination events are widely detected throughout the FHV genome as illustrated using heat maps. (a) Heat maps show the location of junctions within RNA1, within RNA2, or between RNA1 and RNA2. The y-axis corresponds to the last nucleotide of the mapped 5′ strand and the x-axis corresponds to the first nucleotide of the 3′ strand. The number of reads mapping to each event is indicated with a color bar. The red boxes labeled a–i indicate the positions of the junctions in the defective RNAs illustrated in Fig. 1 and are enlarged in (b) for RNA1 and in (c) for RNA2 to show the mapping in these locations. Blue cross-hairs indicate the precise position of the expected junctions.