{
  "assemblies": [
    {
      "name": "hg38",
      "displayName": "Human (hg38)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "hg38-refseq",
        "adapter": {
          "type": "TwoBitAdapter",
          "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.2bit",
          "chromSizes": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chrom.sizes"
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/hg38/bigZips/hg38.chromAlias.txt"
        }
      }
    },
    {
      "name": "panTro6",
      "displayName": "Chimp (panTro6)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "panTro6-refseq",
        "adapter": {
          "type": "TwoBitAdapter",
          "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.2bit",
          "chromSizes": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.chrom.sizes"
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "uri": "https://hgdownload.soe.ucsc.edu/goldenPath/panTro6/bigZips/panTro6.chromAlias.txt"
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "hg38-genes",
      "name": "NCBI RefSeq genes",
      "assemblyNames": ["hg38"],
      "category": ["Genes"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeqCurated.gff.gz"
        },
        "index": {
          "indexType": "CSI",
          "location": {
            "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeqCurated.gff.gz.csi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "hg38-genes-LinearBasicDisplay",
          "heightMode": "grow"
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "panTro6-genes",
      "name": "NCBI RefSeq genes",
      "assemblyNames": ["panTro6"],
      "category": ["Genes"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/ucsc/panTro6/ncbiRefSeq.gff.gz"
        },
        "index": {
          "indexType": "CSI",
          "location": {
            "uri": "https://jbrowse.org/ucsc/panTro6/ncbiRefSeq.gff.gz.csi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "panTro6-genes-LinearBasicDisplay",
          "heightMode": "grow"
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg38-rmsk",
      "name": "RepeatMasker",
      "assemblyNames": ["hg38"],
      "category": ["Repeats"],
      "adapter": {
        "type": "BedTabixAdapter",
        "bedGzLocation": {
          "uri": "https://jbrowse.org/ucsc/hg38/rmsk.bed.gz"
        },
        "index": {
          "indexType": "CSI",
          "location": { "uri": "https://jbrowse.org/ucsc/hg38/rmsk.bed.gz.csi" }
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "hg38-rmsk-LinearBasicDisplay",
          "heightMode": "grow"
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "panTro6-rmsk",
      "name": "RepeatMasker",
      "assemblyNames": ["panTro6"],
      "category": ["Repeats"],
      "adapter": {
        "type": "BedTabixAdapter",
        "bedGzLocation": {
          "uri": "https://jbrowse.org/ucsc/panTro6/rmsk.bed.gz"
        },
        "index": {
          "indexType": "CSI",
          "location": {
            "uri": "https://jbrowse.org/ucsc/panTro6/rmsk.bed.gz.csi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "panTro6-rmsk-LinearBasicDisplay",
          "heightMode": "grow"
        }
      ]
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hg38_panTro6_synteny",
      "name": "Human vs Chimp (UCSC liftOver)",
      "assemblyNames": ["hg38", "panTro6"],
      "adapter": {
        "type": "PairwiseIndexedPAFAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/liftOver/hg38ToPanTro6.over.pif.gz",
        "csi": true,
        "assemblyNames": ["panTro6", "hg38"]
      }
    }
  ]
}