Figure 3. Sequence variation present in the heterogeneous sequences located at the 5′-end of viral mRNAs obtained from infected A549 cells.

For each transcript, the top panel shows the relative nucleotide frequency at each position (log scaled), and the bottom panel shows the Logo representation of the nucleotide variation. The nucleotides are numbered according to the host/virus junction (blue line), defined as the phosphodiester bond located upstream of position G2 on IAV mRNA. The grey bars represent the percentage of the population of reads included in the calculation. Only sequence reads that appeared at least twice were used in the analysis. For all IAV mRNAs, only nucleotide frequencies observed from 15 nt upstream of the G2 and up to 5 nt downstream of G2 are represented. All motifs are represented in the 5′ to 3′ orientation.