{
  "genome_count": 11,
  "loci_count": 1535,
  "variable_locus_count": 1522,
  "paralogous_locus_count": 72,
  "core_threshold": 90,
  "identity": 70,
  "alignment": 50,
  "word_size": 20,
  "outputs": {
    "reference_loci": "reference_loci.tsv",
    "profiles": "profiles.tsv",
    "variable_loci": "variable_loci.tsv",
    "core_loci": "core_loci.tsv",
    "paralogous_loci": "paralogous_loci.tsv",
    "distance_matrix": "distance_matrix.tsv",
    "nexus": "distance_matrix.nex"
  }
}