{
  "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": "hprc_cfhr_HG01109.1.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG01123.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG01123.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "hprc_cfhr_HG01123.1.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG01960.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG01960.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "hprc_cfhr_HG01960.1.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG02055.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG02055.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "hprc_cfhr_HG02055.1.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG00097.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG00097.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "hprc_cfhr_HG00097.1.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG00099.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG00099.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "hprc_cfhr_HG00099.1.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG00128.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG00128.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "hprc_cfhr_HG00128.1.chrom.sizes",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "name": "HG00133.1",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "HG00133.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "ChromSizesAdapter",
          "chromSizesLocation": {
            "uri": "hprc_cfhr_HG00133.1.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_minigraph_bubbles",
      "name": "HPRC release 2 bubbles",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "MinigraphBubbleAdapter",
        "uri": "https://jbrowse.org/demos/hprc/hprc-v2.0-mc-grch38.bubbles.bed.gz",
        "assemblyNameToPanSN": {
          "hg38": "GRCh38"
        }
      },
      "displayDefaults": {
        "color": "rgb(130,130,130)"
      }
    },
    {
      "type": "AlignmentsTrack",
      "trackId": "hprc_minigraph_alleles",
      "name": "HPRC release 2 graph: allele inventory",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "BedTabixAdapter",
        "uri": "https://jbrowse.org/demos/hprc/hprc-v2.0-mc-grch38.alleles.bed.gz"
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "hprc2_wave_grch38",
      "name": "HPRC2 pangenome callset (464 haplotypes)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/pangenomes/freeze/release2/minigraph-cactus/hprc-v2.0-mc-grch38.wave.vcf.gz"
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "displayId": "hprc2_wave_grch38_regular",
          "renderingMode": "phased"
        }
      ]
    },
    {
      "type": "VariantTrack",
      "trackId": "hprc2_pgbi_grch38",
      "name": "HPRC2 pangenome carriage (snarl-level, 462 haplotypes)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/submissions/671F0A25-700C-4DDF-96B0-9668F6C0F25E--hprc_v2.0_mc_grch38_index/hprc-v2.0-mc-grch38.pgbi.vcf.gz"
      },
      "displays": [
        {
          "type": "LinearMultiSampleVariantDisplay",
          "displayId": "hprc2_pgbi_grch38_regular",
          "renderingMode": "phased"
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_minigraph_segments",
      "name": "HPRC release 2 graph (rGFA segments)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/hprc/hprc-v2.0-mc-grch38",
        "assemblyNameToPanSN": {
          "hg38": "GRCh38"
        }
      },
      "displayDefaults": {
        "color": "jexl:get(feature,'rank')==0?'rgb(52,152,219)':'rgb(237,137,44)'"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_cfhr_genes_HG01109_1",
      "name": "HG01109.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG01109.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "hprc_cfhr_HG01109.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_cfhr_genes_HG01123_1",
      "name": "HG01123.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG01123.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "hprc_cfhr_HG01123.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_cfhr_genes_HG01960_1",
      "name": "HG01960.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG01960.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "hprc_cfhr_HG01960.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_cfhr_genes_HG02055_1",
      "name": "HG02055.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG02055.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "hprc_cfhr_HG02055.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_cfhr_genes_HG00097_1",
      "name": "HG00097.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG00097.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "hprc_cfhr_HG00097.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_cfhr_genes_HG00099_1",
      "name": "HG00099.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG00099.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "hprc_cfhr_HG00099.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_cfhr_genes_HG00128_1",
      "name": "HG00128.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG00128.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "hprc_cfhr_HG00128.1.genes.gff3.gz"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hprc_cfhr_genes_HG00133_1",
      "name": "HG00133.1 genes (HPRC release 2 CAT annotation)",
      "assemblyNames": ["HG00133.1"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "hprc_cfhr_HG00133.1.genes.gff3.gz"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_cfhr_synteny_HG01109_1",
      "name": "HG01109.1 vs GRCh38 at CFH (HPRC release 2 alignment)",
      "assemblyNames": ["HG01109.1", "hg38"],
      "adapter": {
        "type": "PAFAdapter",
        "uri": "hprc_cfhr_HG01109.1.paf",
        "queryAssembly": "HG01109.1",
        "targetAssembly": "hg38"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_cfhr_synteny_HG01123_1",
      "name": "HG01123.1 vs GRCh38 at CFH (HPRC release 2 alignment)",
      "assemblyNames": ["HG01123.1", "hg38"],
      "adapter": {
        "type": "PAFAdapter",
        "uri": "hprc_cfhr_HG01123.1.paf",
        "queryAssembly": "HG01123.1",
        "targetAssembly": "hg38"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_cfhr_synteny_HG01960_1",
      "name": "HG01960.1 vs GRCh38 at CFH (HPRC release 2 alignment)",
      "assemblyNames": ["HG01960.1", "hg38"],
      "adapter": {
        "type": "PAFAdapter",
        "uri": "hprc_cfhr_HG01960.1.paf",
        "queryAssembly": "HG01960.1",
        "targetAssembly": "hg38"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_cfhr_synteny_HG02055_1",
      "name": "HG02055.1 vs GRCh38 at CFH (HPRC release 2 alignment)",
      "assemblyNames": ["HG02055.1", "hg38"],
      "adapter": {
        "type": "PAFAdapter",
        "uri": "hprc_cfhr_HG02055.1.paf",
        "queryAssembly": "HG02055.1",
        "targetAssembly": "hg38"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_cfhr_synteny_HG00097_1",
      "name": "HG00097.1 vs GRCh38 at CFH (HPRC release 2 alignment)",
      "assemblyNames": ["HG00097.1", "hg38"],
      "adapter": {
        "type": "PAFAdapter",
        "uri": "hprc_cfhr_HG00097.1.paf",
        "queryAssembly": "HG00097.1",
        "targetAssembly": "hg38"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_cfhr_synteny_HG00099_1",
      "name": "HG00099.1 vs GRCh38 at CFH (HPRC release 2 alignment)",
      "assemblyNames": ["HG00099.1", "hg38"],
      "adapter": {
        "type": "PAFAdapter",
        "uri": "hprc_cfhr_HG00099.1.paf",
        "queryAssembly": "HG00099.1",
        "targetAssembly": "hg38"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_cfhr_synteny_HG00128_1",
      "name": "HG00128.1 vs GRCh38 at CFH (HPRC release 2 alignment)",
      "assemblyNames": ["HG00128.1", "hg38"],
      "adapter": {
        "type": "PAFAdapter",
        "uri": "hprc_cfhr_HG00128.1.paf",
        "queryAssembly": "HG00128.1",
        "targetAssembly": "hg38"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_cfhr_synteny_HG00133_1",
      "name": "HG00133.1 vs GRCh38 at CFH (HPRC release 2 alignment)",
      "assemblyNames": ["HG00133.1", "hg38"],
      "adapter": {
        "type": "PAFAdapter",
        "uri": "hprc_cfhr_HG00133.1.paf",
        "queryAssembly": "HG00133.1",
        "targetAssembly": "hg38"
      }
    },
    {
      "type": "SyntenyTrack",
      "trackId": "hprc_cfhr_multiway",
      "name": "CFH cluster orthologs (hg38 + 8 haplotypes, CAT)",
      "assemblyNames": [
        "hg38",
        "HG00097.1",
        "HG00099.1",
        "HG00128.1",
        "HG00133.1",
        "HG01109.1",
        "HG01123.1",
        "HG01960.1",
        "HG02055.1"
      ],
      "adapter": {
        "type": "MCScanBlocksAdapter",
        "mcscanBlocksLocation": {
          "uri": "hprc_cfhr.blocks",
          "locationType": "UriLocation"
        },
        "blockAssemblies": [
          "hg38",
          "HG01109.1",
          "HG01123.1",
          "HG01960.1",
          "HG02055.1",
          "HG00097.1",
          "HG00099.1",
          "HG00128.1",
          "HG00133.1"
        ],
        "bedLocations": [
          {
            "uri": "hprc_cfhr_hg38.bed",
            "locationType": "UriLocation"
          },
          {
            "uri": "hprc_cfhr_HG01109.1.bed",
            "locationType": "UriLocation"
          },
          {
            "uri": "hprc_cfhr_HG01123.1.bed",
            "locationType": "UriLocation"
          },
          {
            "uri": "hprc_cfhr_HG01960.1.bed",
            "locationType": "UriLocation"
          },
          {
            "uri": "hprc_cfhr_HG02055.1.bed",
            "locationType": "UriLocation"
          },
          {
            "uri": "hprc_cfhr_HG00097.1.bed",
            "locationType": "UriLocation"
          },
          {
            "uri": "hprc_cfhr_HG00099.1.bed",
            "locationType": "UriLocation"
          },
          {
            "uri": "hprc_cfhr_HG00128.1.bed",
            "locationType": "UriLocation"
          },
          {
            "uri": "hprc_cfhr_HG00133.1.bed",
            "locationType": "UriLocation"
          }
        ],
        "assemblyNames": [
          "hg38",
          "HG01109.1",
          "HG01123.1",
          "HG01960.1",
          "HG02055.1",
          "HG00097.1",
          "HG00099.1",
          "HG00128.1",
          "HG00133.1"
        ]
      },
      "displays": [
        {
          "type": "MultiWaySyntenyDisplay",
          "displayId": "hprc_cfhr_multiway-MultiWaySyntenyDisplay"
        }
      ]
    }
  ]
}
