Clustering results among the 50 GT1a ATAHC sequences: genetic distance, percentage of sequences, tree, patristic distance and bootstrap values.

<p><i>Panel i</i>: The genetic distance distribution is shown for both ATAHC sequences (dark colour) and Los Alamos HCV database reference sequences (clear colour). The vertical dotted lines represent the thresholds for clustering, which were estimated by determining the point of overlap/uncertainty region between the two curves of most-closely related (ATAHC sequences) and distantly related (both ATAHC and LANL sequences) for each HCV region. <i>Panel ii</i> shows the ATAHC clustering patterns using Cluster Picker with bootstrap support threshold fixed at 90% and maximum genetic distance threshold varied between 0.01 and 0.08 (colour lines: ATAHC sequences; grey lines: LANL reference sequences). Plain lines represent the percentage of clustered sequences; dot lines correspond to average cluster size. The vertical dot line indicates the clustering threshold (as per panel i) used to determine the percentage of clustered sequences and average cluster size (<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0131437#pone.0131437.t001" target="_blank">Table 1</a>). <i>Panel iii</i> shows the phylloclade with participants highlighted when defined as part of a cluster with the clustering threshold (panel i) and bootstrap support above 90% criteria (Cluster Picker).