{
  "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"
      }
    }
  ],
  "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_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_tier",
      "name": "HPRC release 2 graph: bubble tier (one node per bubble)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "RgfaTabixAdapter",
        "uri": "https://jbrowse.org/demos/hprc/hprc-v2.0-mc-grch38.tier10000",
        "assemblyNameToPanSN": {
          "hg38": "GRCh38"
        }
      }
    },
    {
      "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": "QuantitativeTrack",
      "trackId": "hprc_bubble_score",
      "name": "HPRC release 2 graph: variability (segments per bubble)",
      "assemblyNames": ["hg38"],
      "adapter": {
        "type": "MinigraphBubbleAdapter",
        "uri": "https://jbrowse.org/demos/hprc/hprc-v2.0-mc-grch38.bubbles.bed.gz",
        "assemblyNameToPanSN": {
          "hg38": "GRCh38"
        }
      }
    },
    {
      "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"
        }
      ]
    }
  ]
}