Fig. 5

Analysis of ribosome stalling in ‘Nipponbare’ (NB) and ‘Sea Rice 86’ (SR86) in response to salt stress. a Venn diagram showing common or unique stalling sites in NB under normal (0 h) and salt stress (24 h) conditions. b Venn diagram showing common or unique stalling sites in SR86 under normal (0 h) and salt stress (24 h) conditions. c RPF depth at stalling sites and 20-codon flanking regions is shown in NB and SR86 under normal (0 h) and salt stress (24 h) conditions. The Z-score of ribo-seq depth is shown as the mean of three biological repeats. The number “0” in the x-axis indicates the ribosome stalling site. d The frequency of codons at ribosome stalling sites was compared with their corresponding frequency in gene coding sequences and a hypergeometric test was performed to identify codons with significantly higher occurrence (Q-value <= 0.01) at ribosome stalling sites. The Q-values of hypergeometric tests are shown in the heatmap