{
  "plugins": [
    {
      "name": "GraphGenomeView",
      "esmUrl": "https://jbrowse.org/plugins/jbrowse-plugin-graphgenomeviewer/latest/dist/jbrowse-plugin-graphgenomeviewer.esm.js"
    }
  ],
  "assemblies": [
    {
      "name": "K12",
      "displayName": "E. coli K12",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "K12-ref",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "Sakai",
      "displayName": "E. coli Sakai",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Sakai-ref",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/Sakai.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/Sakai.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/Sakai.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "CFT073",
      "displayName": "E. coli CFT073",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "CFT073-ref",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/CFT073.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/CFT073.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/CFT073.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "NCTC86",
      "displayName": "E. coli NCTC86",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "NCTC86-ref",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/NCTC86.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/NCTC86.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/NCTC86.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "IAI39",
      "displayName": "E. coli IAI39",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "IAI39-ref",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/IAI39.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/IAI39.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/IAI39.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "K12_genes",
      "name": "K12 genes",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/K12.gff.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "Sakai_genes",
      "name": "Sakai genes",
      "assemblyNames": ["Sakai"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/Sakai.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/Sakai.gff.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "CFT073_genes",
      "name": "CFT073 genes",
      "assemblyNames": ["CFT073"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/CFT073.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/CFT073.gff.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "NCTC86_genes",
      "name": "NCTC86 genes",
      "assemblyNames": ["NCTC86"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/NCTC86.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/NCTC86.gff.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "ecoli_pggb_ava",
      "name": "pggb graph: all-vs-all synteny (wfmash)",
      "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"],
      "category": ["Pangenome graph"],
      "adapter": {
        "type": "MultiGenomeIndexedPAFAdapter",
        "pifGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_ava.pif.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_pggb_ava.pif.gz.tbi",
            "locationType": "UriLocation"
          }
        },
        "assemblyNames": ["K12", "Sakai", "CFT073", "NCTC86", "IAI39"]
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "IAI39_genes",
      "name": "IAI39 genes",
      "assemblyNames": ["IAI39"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/ecoli_pangenome/IAI39.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/ecoli_pangenome/IAI39.gff.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "GraphTrack",
      "trackId": "ecoli_minigraph_segments",
      "name": "minigraph graph segments (rGFA)",
      "assemblyNames": ["K12"],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/ecoli_pangenome/ecoli_minigraph"
      },
      "displayDefaults": {
        "color": {
          "field": "rank",
          "scale": "threshold",
          "domain": ["1"],
          "range": ["rgb(52,152,219)", "rgb(237,137,44)"],
          "labels": ["reference", "other assemblies"],
          "title": "Segment rank"
        }
      },
      "displays": [
        {
          "type": "LinearGraphDisplay",
          "displayId": "ecoli_minigraph_segments-LinearGraphDisplay"
        },
        {
          "type": "LinearBasicDisplay",
          "displayId": "ecoli_minigraph_segments-LinearBasicDisplay"
        }
      ]
    }
  ]
}
