{
  "files": {
    "reference": "reference.fasta",
    "pathogenJson": "pathogen.json",
    "genomeAnnotation": "genome_annotation.gff3",
    "treeJson": "tree.json",
    "examples": "sequences.fasta",
    "readme": "README.md",
    "changelog": "CHANGELOG.md"
  },
  "schemaVersion": "3.0.0",
  "defaultCds": "L",
  "attributes": {
    "name": "Lassa Global Tree",
    "reference name": "Josiah",
    "reference accession": "NC_004297"
  },
  "alignmentParams": {
    "penaltyGapExtend": 1,
    "penaltyGapOpen": 8,
    "penaltyGapOpenInFrame": 9,
    "penaltyGapOpenOutOfFrame": 10,
    "penaltyMismatch": 1,
    "scoreMatch": 5,
    "retryReverseComplement": true,
    "allowedMismatches": 10,
    "minSeedCover": 0.12,
    "minLength": 800
  },
  "qc": {
    "missingData": {
      "enabled": true,
      "missingDataThreshold": 20,
      "scoreBias": 4
    },
    "mixedSites": {
      "enabled": true,
      "mixedSitesThreshold": 4
    },
    "frameShifts": {
      "enabled": true
    },
    "stopCodons": {
      "enabled": true
    },
    "privateMutations": {
      "enabled": true,
      "cutoff": 12,
      "typical": 4,
      "weightLabeledSubstitutions": 1,
      "weightReversionSubstitutions": 1,
      "weightUnlabeledSubstitutions": 1
    },
    "snpClusters": {
      "enabled": true,
      "clusterCutOff": 3,
      "scoreWeight": 50,
      "windowSize": 50
    }
  }
}