See Viewing Variants for example IGV visualizations of mutation and related VCF files. For details on how to display mutations in IGV, see Mutation Files.

A MUT file (.mut) is a tab-delimited text file that lists mutations. The first row contains column headings and each subsequent row identifies a mutation. IGV ignores the column headings. It reads the first five columns as shown below and ignores all subsequent columns:

  1. chromosome
  2. start location (location of the first base pair in the mutated region)
  3. end location (location of the last base pair in the mutated region)
  4. sample or patient ID
  5. mutation type (for example, Synonymous, Missense, Nonsense, Indel, etc.)

Example: example.mut

When a specific mutation is moused-over or clicked on, depending on user IGV display settings, a mutation information panel displays the information provided in all the columns of the MUT file, in order, for the particular mutation. For more than ~50 columns of information, only a subset of the information is displayed.