What does a valid mutation site look like? (original) (raw)

The general format of a mutation code is:gene:[ref]coordinates[alt] where gene is a gene code (or nuc for the genomic nucleotide sequence), ref is the nucleotide or amino acids in the reference, alt is the specific nucleotide or amino acid for the mutatant. Either of ref or alt can be missing if no specific state is required.

Rules can either specify [min|max]_[ref|alt|ambig|oth] OR the call required at a mutation e.g. "N:S235F": (not )[ref|alt|ambig|oth]

Valid Mutation Definitions

The following are valid ways to describe variants of each type. We prefer the definition at the top of each list, but provide alternatives for backwards compatibility.

• these are case insensitive e.g. S vs s
• genes can be full e.g. orf1ab spike, or shortened e.g. 1ab, s
• protein based definitions may be acceptable if the reference JSON includes them but may not be shortened e.g. NSP2
• all coordinates are 1-based
• for amino acid mutations, reference can be longer than 1 amino acid

SNP:

• nuc:[ref]nucleotide_coordinate[alt]
• snp:[ref]nucleotide_coordinate[alt]

Amino acid mutation:

• gene:[ref]amino_acid_coordinate_relative_to_gene[alt]
• protein:[ref]amino_acid_coordinate_relative_to_protein[alt]
• gene:[ref]amino_acid_coordinate_relative_to_gene - this allows any other aa to be called as alt
• aa:gene:[ref]amino_acid_coordinate_relative_to_gene[alt]
• aa:protein:[ref]amino_acid_coordinate_relative_to_protein[alt]
• aa:gene:[ref]amino_acid_coordinate_relative_to_gene - this allows any other aa to be called as alt

Deletion:

• del:nucleotide_coordinate:nucleotide_length
• gene:[ref]amino_acid_coordinate-
• gene:[ref]amino_acid_coordinatedel

Insertion (currently parsed but not typed):

• nuc:nucleotide_coordinate+inserted_sequence
• snp:nucleotide_coordinate+inserted_sequence
• gene:amino_acid_coordinate_relative_to_gene+inserted_sequence
• aa:gene:amino_acid_coordinate_relative_to_gene+inserted_sequence

Examples

"nuc:C3037T"
"snp:A27259C"
"orf1ab:P4715L"
"n:RG203KR"
"del:28362:9"
"orf1ab:SGF3675-"