{
  "plugins": [
    {
      "name": "Protein3d",
      "url": "https://jbrowse.org/plugins/jbrowse-plugin-protein3d/latest/dist/jbrowse-plugin-protein3d.umd.production.min.js"
    }
  ],
  "assemblies": [
    {
      "name": "hg38",
      "aliases": ["GRCh38"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "P6R5xbRqRr",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "fastaLocation": {
            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz"
          },
          "faiLocation": {
            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai"
          },
          "gziLocation": {
            "uri": "https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi"
          }
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "location": {
            "uri": "https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/hg38_aliases.txt"
          }
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "gencode.v44.annotation.sorted.gff3",
      "name": "GENCODE v44",
      "category": ["Annotation"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/demos/app/gencode.v44.annotation.sorted.gff3.gz"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/app/gencode.v44.annotation.sorted.gff3.gz.tbi"
          },
          "indexType": "TBI"
        }
      },
      "assemblyNames": ["hg38"]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg38-ncbiRefSeq",
      "name": "NCBI RefSeq - RefSeq All",
      "assemblyNames": ["hg38"],
      "category": ["Genes and Gene Predictions"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz"
        },
        "index": {
          "indexType": "CSI",
          "location": {
            "uri": "https://jbrowse.org/ucsc/hg38/ncbiRefSeq.gff.gz.csi"
          }
        }
      }
    },
    {
      "type": "VariantTrack",
      "trackId": "clinvar_ncbi_hg38",
      "name": "ClinVar variants (NCBI)",
      "assemblyNames": ["hg38"],
      "category": ["Annotation", "ClinVar"],
      "adapter": {
        "type": "VcfTabixAdapter",
        "vcfGzLocation": {
          "uri": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz"
        },
        "index": {
          "location": {
            "uri": "https://ftp.ncbi.nlm.nih.gov/pub/clinvar/vcf_GRCh38/clinvar.vcf.gz.tbi"
          }
        }
      },
      "displays": [
        {
          "type": "LinearVariantDisplay",
          "displayId": "clinvar_ncbi_hg38-LinearVariantDisplay",
          "color": "jexl:({'Benign':'blue','Likely_benign':'deepskyblue','Uncertain_significance':'gray','Pathogenic':'red','Likely_pathogenic':'orange','Conflicting_interpretations_of_pathogenicity':'brown'})[feature.INFO.CLNSIG[0]] || 'purple'"
        }
      ]
    }
  ]
}
