{
  "assemblies": [
    {
      "name": "grape",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "grape-ref",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/grape.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/grape.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/grape.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "location": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/grape.aliases.txt",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "peach",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "peach-ref",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/peach.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/peach.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/peach.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "location": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/peach.aliases.txt",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "cacao",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "cacao-ref",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/cacao.fa.gz",
            "locationType": "UriLocation"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/cacao.fa.gz.fai",
            "locationType": "UriLocation"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/cacao.fa.gz.gzi",
            "locationType": "UriLocation"
          }
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "location": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/cacao.aliases.txt",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "configuration": {
    "disableAnalytics": true
  },
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "grape_genes",
      "name": "Grape genes (NCBI RefSeq GCF_030704535.1)",
      "assemblyNames": ["grape"],
      "category": ["Genes"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/grape_peach_cacao/grape.genes.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/grape.genes.gff3.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "peach_genes",
      "name": "Peach genes (NCBI RefSeq GCF_000346465.2)",
      "assemblyNames": ["peach"],
      "category": ["Genes"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/grape_peach_cacao/peach.genes.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/peach.genes.gff3.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "cacao_genes",
      "name": "Cacao genes (NCBI RefSeq GCF_000208745.1)",
      "assemblyNames": ["cacao"],
      "category": ["Genes"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/grape_peach_cacao/cacao.genes.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/cacao.genes.gff3.gz.tbi",
            "locationType": "UriLocation"
          },
          "indexType": "TBI"
        }
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "grape_peach_cacao_blocks",
      "name": "Grape vs peach, cacao, arabidopsis, poplar, tomato, citrus (MCScan blocks)",
      "_comment_assemblyNames": "The three assemblies this config DECLARES, not the seven columns the table has. A track whose assemblyNames name an assembly the config does not define makes the stacked LinearSyntenyView fail to resolve it, and all three rows come up 'No tracks active'. The extra four are blocks-only mates: they exist in the adapter below, which is what draws their lanes in an LGV, and they need no assembly because a lane is resolved from the table plus that genome's BED.",
      "assemblyNames": ["grape", "peach", "cacao"],
      "category": ["Synteny"],
      "adapter": {
        "type": "MCScanBlocksAdapter",
        "mcscanBlocksLocation": {
          "uri": "https://jbrowse.org/demos/grape_peach_cacao/grape.blocks.gz",
          "locationType": "UriLocation"
        },
        "blockAssemblies": [
          "grape",
          "peach",
          "cacao",
          "arabidopsis",
          "poplar",
          "tomato",
          "citrus"
        ],
        "bedLocations": [
          {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/grape.bed.gz",
            "locationType": "UriLocation"
          },
          {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/peach.bed.gz",
            "locationType": "UriLocation"
          },
          {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/cacao.bed.gz",
            "locationType": "UriLocation"
          },
          {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/arabidopsis.bed.gz",
            "locationType": "UriLocation"
          },
          {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/poplar.bed.gz",
            "locationType": "UriLocation"
          },
          {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/tomato.bed.gz",
            "locationType": "UriLocation"
          },
          {
            "uri": "https://jbrowse.org/demos/grape_peach_cacao/citrus.bed.gz",
            "locationType": "UriLocation"
          }
        ],
        "assemblyNames": [
          "grape",
          "peach",
          "cacao",
          "arabidopsis",
          "poplar",
          "tomato",
          "citrus"
        ]
      }
    }
  ],
  "defaultSession": {
    "name": "Grape / Peach / Cacao multi-way synteny",
    "views": [
      {
        "type": "LinearSyntenyView",
        "displayName": "Peach \u2013 Cacao \u2013 Grape (MCScan blocks)",
        "showColorLegend": false,
        "init": {
          "views": [
            {
              "assembly": "peach"
            },
            {
              "assembly": "cacao"
            },
            {
              "assembly": "grape"
            }
          ],
          "tracks": [
            ["grape_peach_cacao_blocks"],
            ["grape_peach_cacao_blocks"]
          ],
          "colorBy": "reference",
          "autoDiagonalize": true
        }
      }
    ]
  }
}