Figure 2. Read coverage following sequencing of amplicons derived from three regions of the viral genome from six HIV-1 infected subjects.

Eleven amplicons, representing ~4.7kb of of the viral genome were aligned to a patient specific consensus. The position of each amplicons is shown relative to the HXB2 reference genome. The “spikes” in read coverage correspond to regions in which adjacent amplicons overlap. We did not have an amplicon that spanned the region around position 2000.