Figure 2. Identification of recombination events in a single patient and general protocol used for identifying recombination in all patient samples using RDP4.

(A) RDP4 generated recombination schematic indicating evidence of intra-segmental recombination. Regions of recombination events, and corresponding insertions from donor sequences are depicted. Significant sites including nucleotide position(s) involved in recombination are shown for the last recombinant (M_0608_H07). Significant nucleotide positions involved in recombination were checked in a similar fashion for all other recombinants. Recombination events were only considered if at least three recombination analysis methods were in agreement with the obtained results, a p-value of 0.05 or better was obtained, and the consensus recombination score was above the recommended 0.60 value. An example for recombinant M_0608_HO7 showing recombination signals identified by the (B) BOOTSCAN method, (C) RDP method, and (D) GENECONV method are shown. Lastly, the MAXCHI matrices tool when necessary was used to determine the optimal locations of breakpoint pairs, shown in (E). These graphically represent the probabilities of all potential breakpoint pairs that have the best associated p-values displayed by the color key beside the matrix. Dark red peaks indicate the most probable positions of breakpoint pairs, for recombinant M_0608_HO7 these were at nucleotide positions 438 and 733.