Clustering characteristics of different HCV subregions, derived from the Core-HVR1 amplicon and NS5B.

*: Sequence length after alignment and gaps deletion;
$:Genetic distance calculated with ATAHC sequences;
#:Genetic distance threshold estimated from ATAHC pairwise distance distribution;
&:Percentage of sequence clustered using region genetic distance threshold using cluster picker and bootstrap at 90%;
@: Percentage of sequence clustered using pairwise distance threshold (without any bootstrap threshold);
‡: ATAHC sequences with LANL reference sequences.
Characteristics of each subregion were determined after sequence alignment and gaps deletion, including sequence length, H77 sequence location within HCV, genetic diversity calculated from P. Simmonds (as per Fig 1).;clustering threshold estimated from the genetic distance distribution; percentage of sequences clustered at threshold; average cluster size; average patristic distance of identified clusters; average bootstrap values of identified clusters; percentage of sequences clustered using pairwise distance threshold and no bootstrap support.