nextclade_data/data/enpen/enterovirus/cv-a10/pathogen.json at adee3723b83f65a55c9e8fdadf83355b62994be2 · nextstrain/nextclade_data · GitHub

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{
  "$schema": "https://raw.githubusercontent.com/nextstrain/nextclade/refs/heads/release/packages/nextclade-schemas/input-pathogen-json.schema.json",
  "schemaVersion": "3.0.0",
  "files": {
    "reference": "reference.fasta",
    "pathogenJson": "pathogen.json",
    "genomeAnnotation": "genome_annotation.gff3",
    "treeJson": "tree.json",
    "examples": "sequences.fasta",
    "readme": "README.md",
    "changelog": "CHANGELOG.md"
  },
  "attributes": {
    "name": "Coxsackievirus A10",
    "reference name": "Human coxsackievirus A10 strain Kowalik, complete genome",
    "reference accession": "AY421767.1"
  },
  "alignmentParams": {
        "penalityGapExtend": 3,
        "penaltyGapOpen": 13,
        "penaltyGapOpenInFrame": 18,
        "penaltyGapOpenOutOfFrame": 23,
        "kmerLength": 6,
        "kmerDistance": 25,
        "minMatchLength": 30,
        "allowedMismatches": 10,
        "minLength": 100,
        "minSeedCover": 0.30
    },
  "defaultCds": "VP1",
  "compatibility": {
        "cli": "3.0.0-alpha.0",
        "web": "3.0.0-alpha.0"
    },
  "mutLabels": {
    "nucMutLabelMap": {
      }
    },
  "qc": {
    "frameShifts": {
      "enabled": true,
      "scoreWeight": 100
    },
    "missingData": {
      "enabled": true,
      "missingDataThreshold": 500,
      "scoreBias": 100
    },
    "mixedSites": {
      "enabled": true,
      "mixedSitesThreshold": 20
    },
    "privateMutations": {
      "cutoff": 200,
      "enabled": true,
      "typical": 100,
      "weightLabeledSubstitutions": 1.5,
      "weightReversionSubstitutions": 2,
      "weightUnlabeledSubstitutions": 1
    },
    "stopCodons": {
      "enabled": true,
      "scoreWeight": 40
    },
    "divergence": {
      "enabled": true,
      "maxDivergence": 0.15,
      "scoreWeight": 50
    },
    "recombinants": {
      "enabled": true,
      "mutationsThreshold": 140,
      "scoreWeight": 50
    }
    },
  "cdsOrderPreference":["VP4", "VP2", "VP3", "VP1", "2A", "2B", "2C", "3A", "3B", "3C", "3D"]

}