SNP output file

SNP File (snp.tsv)

Taranis provides SNP information for each core gene that made exact match or inferred a new allele (INF) inside the snp.tsv file. It is a tab separation file containing the following columns:

Core Name	Sample Name	Allele Number	Position	Mutation Schema/Sample

Codon Schema/Sample	Protein Schema/Sample	Missense/Synonymous

Annotation Schema/Sample

Core Name

It is the file name in your schema.

Sample Name

It is the file name of the samples.

Allele Number

Number of the allele that is doing an exact match with the sample

Position

SNP position on the core gene

Mutation Schema/Sample

Displays the nucleotide different from the schema and the sample

Codon Schema/Sample

Displays the Schema and the Sample codon

Protein Schema/Sample

Displays the protein created by Schema and Sample codon .

Missense/Synonymous column

A synonymous substitution (often called a silent substitution though they are not always silent) is the evolutionary substitution of one base for another in an exon of a gene coding for a protein, such that the produced amino acid sequence is not modified.

A nonsynonymous substitution is a nucleotide mutation that alters the amino acid sequence of a protein. Nonsynonymous substitutions differ from synonymous substitutions, which do not alter amino acid sequences and are (sometimes) silent mutations. As nonsynonymous substitutions result in a biological change in the organism.

There are several common types of nonsynonymous substitutions.

• Missense mutations are nonsynonymous substitutions that arise from point mutations, mutations in a single nucleotide that result in the substitution of a different amino acid, resulting in a change to the protein encoded. Missense mutation or refers to a change in one amino acid in a protein, arising from a point mutation in a single nucleotide.

• Nonsense mutations are nonsynonymous substitutions that arise when a mutation in the DNA sequence causes a protein to terminate prematurely by changing the original amino acid to a stop codon. Another type of mutation that deals with stop codons is known as a readthrough mutation, which occurs when a stop codon is exchanged for an amino acid codon, causing the protein to be longer than specified

Annotation Schema/Sample

Displays the group type of the amino acid. The possible values are polar,nonpolar,acid and basic.