{
  "plugins": [
    {
      "name": "GraphGenomeView",
      "esmUrl": "https://jbrowse.org/demos/graphgenomeviewer/jbrowse-plugin-graphgenomeviewer.esm.js"
    }
  ],
  "assemblies": [
    {
      "name": "hg38",
      "aliases": ["GRCh38"],
      "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz",
      "refNameAliases": {
        "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
      }
    },
    {
      "name": "HG01109.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG01109.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "HG01109.1.gfa.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG01123.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG01123.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "HG01123.1.gfa.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG01960.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG01960.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "HG01960.1.gfa.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG02055.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG02055.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "HG02055.1.gfa.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG00097.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG00097.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "HG00097.1.gfa.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG00099.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG00099.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "HG00099.1.gfa.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG00128.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG00128.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "HG00128.1.gfa.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG00133.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG00133.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "HG00133.1.gfa.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "hg38_ncbiRefSeq_ucsc",
      "name": "NCBI RefSeq genes (hg38)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz",
        "csi": true
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_genes_HG01109_1",
      "name": "HG01109.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG01109.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "HG01109.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_genes_HG01123_1",
      "name": "HG01123.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG01123.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "HG01123.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_genes_HG01960_1",
      "name": "HG01960.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG01960.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "HG01960.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_genes_HG02055_1",
      "name": "HG02055.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG02055.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "HG02055.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_genes_HG00097_1",
      "name": "HG00097.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG00097.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "HG00097.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_genes_HG00099_1",
      "name": "HG00099.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG00099.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "HG00099.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_genes_HG00128_1",
      "name": "HG00128.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG00128.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "HG00128.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_genes_HG00133_1",
      "name": "HG00133.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG00133.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "HG00133.1.genes.gff3.gz"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_multiway",
      "name": "HPRC haplotypes vs GRCh38 (hg38 + 8 haplotypes, unpacked from the release 2 GFA)",
      "assemblyNames": [
        "hg38",
        "HG01109.1",
        "HG01123.1",
        "HG01960.1",
        "HG02055.1",
        "HG00097.1",
        "HG00099.1",
        "HG00128.1",
        "HG00133.1"
      ],
      "adapter": {
        "type": "MultiGenomeIndexedPAFAdapter",
        "uri": "hprc_multiway_gfa.pif.gz",
        "csi": true,
        "assemblyNames": [
          "hg38",
          "HG01109.1",
          "HG01123.1",
          "HG01960.1",
          "HG02055.1",
          "HG00097.1",
          "HG00099.1",
          "HG00128.1",
          "HG00133.1"
        ],
        "assemblyNameToPanSN": {
          "hg38": "GRCh38#0",
          "HG01109.1": "HG01109#1",
          "HG01123.1": "HG01123#1",
          "HG01960.1": "HG01960#1",
          "HG02055.1": "HG02055#1",
          "HG00097.1": "HG00097#1",
          "HG00099.1": "HG00099#1",
          "HG00128.1": "HG00128#1",
          "HG00133.1": "HG00133#1"
        }
      },
      "displays": [
        {
          "type": "MultiWaySyntenyDisplay",
          "displayId": "hprc_multiway-MultiWaySyntenyDisplay",
          "height": 200
        }
      ]
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_v2_1_gbz",
      "name": "HPRC release 2.1 haplotypes vs GRCh38, read from the graph (gbz-base)",
      "assemblyNames": [
        "hg38",
        "HG00097.1",
        "HG00099.1",
        "HG00128.1",
        "HG00133.1",
        "HG01109.1",
        "HG01123.1",
        "HG01960.1",
        "HG02055.1"
      ],
      "adapter": {
        "type": "GbzBaseSyntenyAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/v2.1/hprc-v2.1-mc-grch38/hprc-v2.1-mc-grch38.gbz.db",
        "haplotypeIndexLocation": {
          "uri": "https://jbrowse.org/demos/hprc/hprc-v2.1-mc-grch38.haplotype-index.db"
        },
        "assemblyNames": [
          "hg38",
          "HG00097.1",
          "HG00099.1",
          "HG00128.1",
          "HG00133.1",
          "HG01109.1",
          "HG01123.1",
          "HG01960.1",
          "HG02055.1"
        ],
        "assemblyNameToPanSN": {
          "hg38": "GRCh38#0",
          "HG00097.1": "HG00097#1",
          "HG00099.1": "HG00099#1",
          "HG00128.1": "HG00128#1",
          "HG00133.1": "HG00133#1",
          "HG01109.1": "HG01109#1",
          "HG01123.1": "HG01123#1",
          "HG01960.1": "HG01960#1",
          "HG02055.1": "HG02055#1"
        },
        "context": 1000,
        "nodeLimit": 50000
      },
      "displays": [
        {
          "type": "MultiWaySyntenyDisplay",
          "displayId": "hprc_v2_1_gbz-MultiWaySyntenyDisplay",
          "height": 600,
          "lanes": [
            "HG00097.1",
            "HG00099.1",
            "HG00128.1",
            "HG00133.1",
            "HG01109.1",
            "HG01123.1",
            "HG01960.1",
            "HG02055.1"
          ]
        }
      ]
    }
  ],
  "defaultSession": {
    "name": "HPRC haplotypes vs GRCh38",
    "views": [
      {
        "type": "LinearGenomeView",
        "assembly": "hg38",
        "loc": "chr20:44,580,000-44,680,000",
        "tracks": ["hg38_ncbiRefSeq_ucsc", "hprc_multiway", "hprc_v2_1_gbz"]
      }
    ]
  }
}
