Extended Data Fig. 10: Characteristics of novel predicted ORFs.

a, b, Scatter plots presenting the correlation between translation levels as estimated by our curated quantification and as calculated by ORF-RATER for Vero (a) and Calu3 cells (b). Points representing canonical ORFs are outlined in black. Spearman’s R is presented. c, d, Read densities over ORF-N as measured by the different Ribo-seq approaches in two replicates in Vero cells at 5 hpi (c) and Calu3 cells at 7 hpi (d). The read densities are shown with different colours indicating the three frames relative to the main ORF in each figure (red, frame 0; black, frame +1; grey, frame +2). Filled and open rectangles indicate the canonical and novel ORFs, respectively. ORF14 location is marked based on the homology to SARS-CoV. e, Transmembrane region predicted in S.iORF1 using Phobius. f, Transmembrane region predicted in ORF3c (3a.iORF1) using Phobius. g, Signal peptide prediction in 3a.iORF2 as predicted using Phobius. h, i, Read densities over ORF3a as measured by the different ribosome profiling approaches in two replicates in Vero cells at 5 hpi (h) and Calu3 cells at 7 hpi (i). The read densities are shown with different colours indicating the three frames relative to the main ORF in each figure (red, frame 0; black, frame +1; grey, frame +2). Filled and open rectangles indicate the canonical and novel ORFs, respectively. ORF3b and extended iORF2 are marked based on the homology to SARS-CoV.