Fig. 2.

Covarying sites (P < 0.001) in the HCV genome represented as coordinates. Open diamonds indicate that one or both sites fall within an epitope or at an association site, and dark diamonds indicate that the sites do not fall within either. Many covariant sites fall in close proximity to one another in the genome (illustrated by the linear trend); however, there are groupings that suggest strong covariation between residues within NS5A and residues within other proteins. Sequence coverage was not found to be a function of covariant site identification.