A visual representation of a portion of a 1.4-gigabase, 4.5-million-sequence nucleotide alignment, derived from overlapping 454 reads covering nearly the complete HIV-1 genome, from 35 individual PCR amplicons from a single patient at 5 time-points during infection. The “fin-like” structures reflect the length distributions of reads that begin at each primer site (left-to-right for forward reads, above midline; right-to-left for reverse reads, below midline). In the original image, which has been reduced for printing, each pixel corresponds to a single nucleotide (A, red; C, blue; G, black; T, green). Each vertical grid line represents 5,000 sequence reads; each horizontal grid line, 50 base pairs. The overall number of reads across the genome was fairly constant, indicating similar primer design success and data richness for genetic variability assessments.
Brodin et al. BMC Bioinformatics 2013 14:255 doi:10.1186/1471-2105-14-255