{
  "assemblies": [
    {
      "name": "rice",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "rice-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "rice.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "sorghum",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "sorghum-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "sorghum.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "maize",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "maize-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "maize.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "brachypodium",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "brachypodium-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "brachypodium.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "setaria",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "setaria-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "setaria.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "configuration": {},
  "connections": [],
  "defaultSession": {
    "name": "Grasses orthology synteny",
    "views": [
      {
        "type": "LinearSyntenyView",
        "displayName": "rice - sorghum - maize - brachypodium - setaria (OrthoFinder orthogroups)",
        "showColorLegend": false,
        "init": {
          "views": [
            {
              "assembly": "rice"
            },
            {
              "assembly": "sorghum"
            },
            {
              "assembly": "maize"
            },
            {
              "assembly": "brachypodium"
            },
            {
              "assembly": "setaria"
            }
          ],
          "tracks": [
            ["grasses_orthogroups"],
            ["grasses_orthogroups"],
            ["grasses_orthogroups"],
            ["grasses_orthogroups"]
          ],
          "colorBy": "reference",
          "autoDiagonalize": true,
          "sameScale": true,
          "collapseEmptyRows": true
        }
      }
    ]
  },
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "rice_genes",
      "name": "rice genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "rice.sorted.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "rice.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": ["rice"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "sorghum_genes",
      "name": "sorghum genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "sorghum.sorted.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "sorghum.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": ["sorghum"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "maize_genes",
      "name": "maize genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "maize.sorted.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "maize.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": ["maize"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "brachypodium_genes",
      "name": "brachypodium genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "brachypodium.sorted.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "brachypodium.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": ["brachypodium"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "setaria_genes",
      "name": "setaria genes",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "setaria.sorted.gff3.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "setaria.sorted.gff3.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "assemblyNames": ["setaria"]
    },
    {
      "type": "SyntenyTrack",
      "trackId": "grasses_orthogroups",
      "name": "Grasses orthogroups (OrthoFinder)",
      "assemblyNames": ["rice", "sorghum", "maize", "brachypodium", "setaria"],
      "adapter": {
        "type": "MCScanBlocksAdapter",
        "uri": "rice.blocks.gz",
        "blockAssemblies": [
          "brachypodium",
          "maize",
          "rice",
          "setaria",
          "sorghum"
        ],
        "bedLocations": [
          {
            "uri": "brachypodium.bed.gz"
          },
          {
            "uri": "maize.bed.gz"
          },
          {
            "uri": "rice.bed.gz"
          },
          {
            "uri": "setaria.bed.gz"
          },
          {
            "uri": "sorghum.bed.gz"
          }
        ],
        "assemblyNames": ["rice", "sorghum", "maize", "brachypodium", "setaria"]
      }
    }
  ]
}