Alt text
Figure 2: The 5 end codon identity of footprints influences read abundance and reading frame fidelity. (a) The top panel depicts the mRNA tunnel on the small ribosome subunit. Red arrow indicates the 5′ end of RPF generated by Ribo-seq. RPFs from HEK293 cells are stratified by the identity of codons at different positions of footprints. Their corresponding IFR values (middle panel) and abundance (bottom panel) are group plotted. Red line, mean ± SD. (b) RPFs are grouped based on the codon identity at A-site, P-site, and 5′ end of footprints. All 61 sense codons are plotted by the average codon coverage score of RPFs (x-axis) against the average in-frame rate (y-axis). (c) Metagene analysis of RPFs obtained from HEK293 cells. Transcripts are aligned at the annotated start codon (1st AUG, green triangle) or internal AUG codons (blank triangle). The average read density at each nucleotide position is plotted using the P-site of RPFs stratified by reading frames (magenta, frame 0; blue, frame 1; green, frame 2). The aligned codon is highlighted, which corresponds to the 5′ end of footprints when the P-site is at the +12 codon position.