Major <i>in vitro</i> recombinant haplotypes assigned by ShoRAH.

<p>Haplotypes were aligned to the five reference strains and characterized. The top part shows the five virus strains (true haplotypes) of the 5-virus-mix and the bars indicate the specific mutation for each strain distinguishing it from the other four virus strains. The corresponding nucleotides and positions are indicated. HIV-1_HXB2 has one unique mutation at position 84 (reference numbering 2362) that is indicated in grey. The mutations for HIV-1_NL4-3 are marked in blue, in HIV-1_JR-CSF in green, in HIV-1_89.6 in red, and in HIV-1_YU2 in orange. Dark colours indicate unique mutations, light colours indicate differences to other strains but not unique for the respective strain. The bottom part shows all recombinant haplotypes found at 1% and higher frequencies. Triangles indicate positions were a specific nucleotide is expected according to the corresponding strain, but is missing. The Nucleotide positions in the sequences are indicated.