Hi Anna,
thank you for this! VIGOR4 is easy to use, which is great, and the output table is very clear. I’m glad you’ve annotated all of these.
I tested it and I note that for the results for ORF3d, it says “no evidence of expression”, but I think that there is evidence of expression at least for the shorter form of the ORF, which we term “ORF3d-2” - see Finkel et al. “The coding capacity of SARS-CoV-2” Supp. Tables 4 & 5. Likewise for ORF10. In any case, the evidence for expression of the excluded ORF2b (S.iORF1 or 2) appears to be stronger than for these ORFs, from this data.
Of course, what counts as sufficient evidence will be debatable, and all of these ORFs deserve further study! For such ORFs inferred to be weakly expressed on the basis of ribosome profiling data (or other lines of evidence such as immunological or evolutionary data, as e.g. mentioned in our eLife paper), I would personally recommend a weaker claim than “no evidence”, such as “evidence for expression ambiguous” or “expression status ambiguous”.
Zachary