{
  "$schema": "https://jbrowse.org/jb2/schema/v5/config.json",
  "assemblies": [
    {
      "name": "Col-0",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Col-0-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "uri": "Col-0.chrom.sizes"
        }
      }
    },
    {
      "name": "Ler",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Ler-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "uri": "Ler.chrom.sizes"
        }
      }
    },
    {
      "name": "Cvi",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Cvi-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "uri": "Cvi.chrom.sizes"
        }
      }
    },
    {
      "name": "Eri",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Eri-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "uri": "Eri.chrom.sizes"
        }
      }
    },
    {
      "name": "Kyo",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Kyo-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "uri": "Kyo.chrom.sizes"
        }
      }
    },
    {
      "name": "Sha",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "Sha-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "uri": "Sha.chrom.sizes"
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "SyntenyTrack",
      "trackId": "syri_pangenome",
      "name": "SyRI regions",
      "assemblyNames": ["Col-0", "Ler", "Cvi", "Eri", "Kyo", "Sha"],
      "adapter": {
        "type": "MultiGenomePAFAdapter",
        "uri": "syri_pangenome.paf",
        "attributeColumns": ["syri", "color"]
      },
      "displays": [
        {
          "type": "MultiWaySyntenyDisplay",
          "displayId": "syri_pangenome-MultiWaySyntenyDisplay",
          "rows": { "domain": ["Ler", "Cvi", "Eri", "Kyo", "Sha"] },
          "ribbonColor": {
            "field": "syri",
            "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
          }
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "syri_regions_on_Col-0",
      "name": "SyRI regions on Col-0, by accession",
      "assemblyNames": ["Col-0"],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "syri_regions.bed.gz",
        "disableGeneHeuristic": true
      },
      "displays": [
        {
          "type": "LinearMultiRowFeatureDisplay",
          "displayId": "syri_regions_on_Col-0-LinearMultiRowFeatureDisplay",
          "rows": {
            "field": "query",
            "domain": ["Ler", "Cvi", "Eri", "Kyo", "Sha"]
          },
          "color": {
            "domain": ["SYN", "INV", "TRANS", "INVTR", "DUP", "INVDP"]
          }
        }
      ]
    }
  ]
}