Figure 2

Overlap graph. Example of amplicon sampling from a quasispecies constituted by two variants (binary alphabet), with different prevalence. The reads are aligned to a reference genome, cover entirely an amplicon and are trimmed to the amplicon start/end positions (otherwise a question mark is placed). With such a design of 4 amplicons and 3 overlaps, the last overlap allows for ambiguous consistency. The overlap graph analysis leads to the reconstruction of 4 candidate variants, where 2 of them are in-silico recombinants. Without additional analysis on read distributions over the amplicons, it is impossible to infer the correct quasispecies.