Fig 5. Visualisation of #105B Illumina recombinant type.

(A) Recombinants detected via Illumina sequencing were plotted by type for p0, p2, p7, and p12; precise (open black circles), imprecise-insertion (open blue circles) or imprecise-deletion (open red circles). All recombinants detected with Oxford Nanopore as well as Illumina sequencing, irrespective of passage number, are indicated as precise (open black triangles) or imprecise-insertion (open blue triangles) recombinants. (B) Recombinant counts. The total number of independent junctions at each passage (left Y axis) was plotted against the passage number (x-axis) highlighting the level of diversity within the population at each passage. The proportion of #105B at each passage was plotted as a percentage of the total reads for #105B at p0 and after normalisation of all reads to p0 (right Y axis). (C) Comparison of the percentage of in-frame and out-of-frame recombinants present at each passage.