SNP Mutator

Generate mutated sequence files from a reference genome.

SNP Mutator was developed by the United States Food and Drug Administration, Center for Food Safety and Applied Nutrition.


  • Reads a fasta file and generates any number of mutated fasta replicate files.
  • Mutations can be any number of single-base substitutions, insertions, and deletions at randomly chosen positions, uniformly distributed across the genome.
  • Mutations can be chosen from a subset (pool) of all possible positions.
  • Replicates can be partitioned into multiple groups with each group sharing a pool of eligible positions.
  • Generates a summary file listing the original base and the mutation for all mutated positions.
  • Mutations can be either monomorphic or polymorphic.
  • VCF file generation.
  • Various metrics can be saved to an output file.
  • The fasta defline sequence id can be customized.


See the LICENSE file included in the SNP Mutator distribution.