Fig. 2
From: Long range PCR-based deep sequencing for haplotype determination in mixed HCMV infections
Haplotype diversity of two polymorphic regions, F3 and F4 determined by PacBio sequencing. Shown are sequence alignments of the two polymorphic amplified regions F3 and F4 and their genetic diversity. Top: Haplotype alignments for region F3, Bottom: Haplotype alignments for region F4. Each figure consists of three separate tracks. Alignments of F3 cover a 7.7 kb region (from UL72 to UL76) and F4 alignments cover a 6.7 kb region (from UL146 to UL139). In the top track, annotated CDS and genotypes are depicted with grey or blue arrows, respectively; Track 2: The mean pairwise identity over all pairs in the column is depicted. Green: 100% identity, greenish-brown: at least 30% identity but less than 100%, red: less than 30%; Track 3: Lanes 1–8 or 1–9: Haplotypes sequences, hap, of all bronchoalveolar lavages, BAL, are depicted. Variants are shown in black. Annotations and alignments were generated with geneious prime 2019.0.3