Should all annotations for a modified
...
nucleotide be included within the sequence listing, or can there be included a reference to a table in the description instead?
The A sequence in a sequence listing should be comprehensive and include all of the necessary annotations so it should not provide details of the modified residue/s in the description only.feature keys, qualifiers, and qualifier values to accurately represent the sequence without the need to refer to an external document. It is not acceptable to define a modified nucleotide by referring to a table or paragraph in the patent application description. The sequence listing should not rely on a reference to any external source of information, for example a table in the description of the patent specification.
As you note, WIPO ST.26 strongly recommends that the sequence should contain the unmodified nucleotide (or if not possible variable ‘n’) and a modified base feature. If there is a specific modified nucleotide which is not listed in Part 2 of Annex I of ST.26, then there should be both:
...
Otherwise there are modifications which are missing from the resulting sequence listing sequences once it is published as part of the INSDC database, for instance.