{
  "schemaVersion": "1.2.0",
  "privateMutations": {
    "enabled": true,
    "typical": 5,
    "cutoff": 10
  },
  "missingData": {
    "enabled": true,
    "missingDataThreshold": 10,
    "scoreBias": 300
  },
  "snpClusters": {
    "enabled": true,
    "windowSize": 100,
    "clusterCutOff": 1,
    "scoreWeight": 20
  },
  "mixedSites": {
    "enabled": true,
    "mixedSitesThreshold": 5
  },
  "frameShifts": {
    "enabled": true,
    "ignoredFrameShifts": [
      { "geneName": "ORF3a", "codonRange": {"begin": 256, "end": 276} },
      { "geneName": "ORF3a", "codonRange": {"begin": 258, "end": 276} },
      { "geneName": "ORF7a", "codonRange": {"begin": 61, "end": 122} },
      { "geneName": "ORF7a", "codonRange": {"begin": 62, "end": 122} },
      { "geneName": "ORF7a", "codonRange": {"begin": 76, "end": 122} },
      { "geneName": "ORF7a", "codonRange": {"begin": 101, "end": 122} },
      { "geneName": "ORF7b", "codonRange": {"begin": 41, "end": 44} },
      { "geneName": "ORF8", "codonRange": {"begin": 107, "end": 122} },
      { "geneName": "ORF8", "codonRange": {"begin": 119, "end": 122} },
      { "geneName": "ORF8", "codonRange": {"begin": 120, "end": 122} },
      { "geneName": "ORF8", "codonRange": {"begin": 121, "end": 123} }
    ]
  },
  "stopCodons": {
    "enabled": true,
    "ignoredStopCodons": [
      {"geneName": "ORF7a", "codon": 61},
      {"geneName": "ORF7a", "codon": 93},
      {"geneName": "ORF7b", "codon": 32},
      {"geneName": "ORF7b", "codon": 38},
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      {"geneName": "ORF8", "codon": 18},
      {"geneName": "ORF8", "codon": 25},
      {"geneName": "ORF8", "codon": 26},
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      {"geneName": "ORF8", "codon": 66},
      {"geneName": "ORF8", "codon": 67},
      {"geneName": "ORF8", "codon": 105}
    ]
  }
}