Catalogue of mutations

Also referred to as a "panel" sometimes. This is the catalogue of mutations that confer resistance (or susceptibility). Provided via the -i/--panel option.

This file is a tab-delimited (TSV) file with four columns

  1. The gene name of the mutation
  2. The mutation in the form <ref><pos><alt>, where <ref> is the reference nucleotide or amino acid, <pos> is the 1-based position in the gene/protein, and <alt> is the nucleotide or amino acid the reference is changed to. <pos> is with respect to the type of mutation - i.e. if the mutation is a amino acid change, the <pos> must be position within the protein (codon position). Promoter mutations can be specied with a negative symbol - e.g. -10 means 10 nucleotide before the first position in the gene. One-letter codes are to be used for amino acids.
  3. The residue type - DNA (nucleotide change) or PROT (amino acid change).
  4. Comma-separated list of the drug(s) the mutation confers resistance to. Use NONE if the mutation is not associated with resistance.

Example

pncA    TCG196TAG   DNA Pyrazinamide
pncA    T142R   PROT    Pyrazinamide
tlyA    S159*   PROT    Capreomycin
embB    M306N   PROT    Ethambutol
rpoB    C1275CCA    DNA Rifampicin
gid R137P   PROT    Streptomycin
gid R118S   PROT    Streptomycin
tlyA    G123GC  DNA Capreomycin
pncA    G97D    PROT    Pyrazinamide
fabG1   C-15X   DNA Ethionamide,Isoniazid