Figure 2. Impact of GC and homopolymers content on the
sequencing coverage of the recombinant AAV genome. (a)Sequencing coverage and percentage of GC along the AAV vector genome.
The sequencing coverages obtained from the 3.2-kb AAV8-CAG-GFP vector
(red) and the internal normalizer (vector plasmid) (blue) were
normalized by dividing the read coverage at each base by the sum of the
coverage for all bases mapped along the rAAV genome. The grey boxes
indicate two 300 bp-regions showing a drastic sequencing coverage drop.
Region 1 and 2 were centered around the minimal number of reads at
position 666 and 1421 of the rAAV genome, respectively. The percentage
of GC (black) was determined using the program NTContent with the
following parameters: window size, 200 bases and step, 20 bases. The
rAAV genome map is represented above the graph. (b, c)Nucleotide content along regions 1 (b) and 2 (c). Each base was
represented at each position by a colored dot: G (green), C (brown), T
(blue) and A (purple). Colored boxes represent homopolymers of ≥ 6
nucleotides. Magnified sequencing coverages are represented as black
lines.