{
  "assemblies": [
    {
      "name": "GCF_025998455.1",
      "displayName": "Helicobacter pylori (CHC155 2022)",
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "metadata": {
          "blatDb": "GCF_025998455.1",
          "ucsc": {
            "genome": "GCF_025998455.1",
            "taxId": "210",
            "groups": "groups.txt",
            "description": "Helicobacter pylori (CHC155 2022)",
            "twoBitPath": "GCF_025998455.1.2bit",
            "twoBitBptUrl": "GCF_025998455.1.2bit.bpt",
            "chromSizes": "GCF_025998455.1.chrom.sizes.txt",
            "chromAliasBb": "GCF_025998455.1.chromAlias.bb",
            "organism": "ASM2599845v1 Oct. 2022",
            "defaultPos": "NZ_AP026446.1:565533-575533",
            "scientificName": "Helicobacter pylori",
            "htmlPath": "<a href=\"https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/html/GCF_025998455.1_ASM2599845v1.description.html\">html/GCF_025998455.1_ASM2599845v1.description.html</a>",
            "blat": "dynablat-01.soe.ucsc.edu 4040 dynamic GCF/025/998/455/GCF_025998455.1",
            "transBlat": "dynablat-01.soe.ucsc.edu 4040 dynamic GCF/025/998/455/GCF_025998455.1",
            "isPcr": "dynablat-01.soe.ucsc.edu 4040 dynamic GCF/025/998/455/GCF_025998455.1"
          }
        },
        "trackId": "GCF_025998455.1-ReferenceSequenceTrack",
        "adapter": {
          "type": "TwoBitAdapter",
          "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/GCF_025998455.1.2bit",
          "chromSizes": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/GCF_025998455.1.chrom.sizes.txt"
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "refNameColumnHeaderName": "ucsc",
          "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/GCF_025998455.1.chromAlias.txt"
        }
      },
      "geneticCodes": {
        "NZ_AP026446.1": 11
      }
    }
  ],
  "tracks": [
    {
      "metadata": {
        "ucsc": {
          "track": "assembly",
          "longLabel": "Assembly",
          "shortLabel": "Assembly",
          "visibility": "hide",
          "colorByStrand": "150,100,30 230,170,40",
          "color": "150,100,30",
          "altColor": "230,170,40",
          "bigDataUrl": "bbi/GCF_025998455.1_ASM2599845v1.assembly.bb",
          "type": "bigBed 6",
          "html": "<a href=\"https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/html/GCF_025998455.1_ASM2599845v1.assembly\">html/GCF_025998455.1_ASM2599845v1.assembly</a>",
          "searchIndex": "name",
          "searchTrix": "ixIxx/GCF_025998455.1_ASM2599845v1.assembly.ix",
          "url": "https://www.ncbi.nlm.nih.gov/nuccore/$$",
          "urlLabel": "NCBI Nucleotide database:",
          "group": "map"
        }
      },
      "category": ["Mapping and Sequencing"],
      "trackId": "GCF_025998455.1-assembly",
      "description": "Assembly",
      "assemblyNames": ["GCF_025998455.1"],
      "name": "Assembly",
      "type": "FeatureTrack",
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/bbi/GCF_025998455.1_ASM2599845v1.assembly.bb"
      }
    },
    {
      "metadata": {
        "ucsc": {
          "track": "cytoBandIdeo",
          "shortLabel": "Chromosome Band (Ideogram)",
          "longLabel": "Ideogram for Orientation",
          "group": "map",
          "visibility": "dense",
          "type": "bigBed 4 +",
          "bigDataUrl": "bbi/GCF_025998455.1_ASM2599845v1.cytoBand.bb"
        }
      },
      "category": ["Mapping and Sequencing"],
      "trackId": "GCF_025998455.1-cytoBandIdeo",
      "description": "Ideogram for Orientation",
      "assemblyNames": ["GCF_025998455.1"],
      "name": "Chromosome Band (Ideogram)",
      "type": "FeatureTrack",
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/bbi/GCF_025998455.1_ASM2599845v1.cytoBand.bb"
      }
    },
    {
      "metadata": {
        "ucsc": {
          "track": "gc5Base",
          "shortLabel": "GC Percent",
          "longLabel": "GC Percent in 5-Base Windows",
          "group": "map",
          "visibility": "dense",
          "autoScale": "Off",
          "maxHeightPixels": "128:36:16",
          "graphTypeDefault": "Bar",
          "gridDefault": "OFF",
          "windowingFunction": "Mean",
          "color": "0,0,0",
          "altColor": "128,128,128",
          "viewLimits": "30:70",
          "type": "bigWig 0 100",
          "bigDataUrl": "bbi/GCF_025998455.1_ASM2599845v1.gc5Base.bw",
          "html": "<a href=\"https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/html/GCF_025998455.1_ASM2599845v1.gc5Base\">html/GCF_025998455.1_ASM2599845v1.gc5Base</a>"
        }
      },
      "category": ["Mapping and Sequencing"],
      "trackId": "GCF_025998455.1-gc5Base",
      "description": "GC Percent in 5-Base Windows",
      "assemblyNames": ["GCF_025998455.1"],
      "name": "GC Percent",
      "type": "QuantitativeTrack",
      "adapter": {
        "type": "BigWigAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/bbi/GCF_025998455.1_ASM2599845v1.gc5Base.bw"
      }
    },
    {
      "metadata": {
        "ucsc": {
          "track": "tandemDups",
          "parent": "tanDups on",
          "shortLabel": "Tandem Dups",
          "longLabel": "Paired exactly identical sequence survey over entire genome assembly",
          "bigDataUrl": "bbi/GCF_025998455.1_ASM2599845v1.tandemDups.bb",
          "type": "bigBed 12"
        }
      },
      "category": ["Mapping and Sequencing"],
      "trackId": "GCF_025998455.1-tandemDups",
      "description": "Paired exactly identical sequence survey over entire genome assembly",
      "assemblyNames": ["GCF_025998455.1"],
      "name": "Tandem Dups",
      "type": "FeatureTrack",
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/bbi/GCF_025998455.1_ASM2599845v1.tandemDups.bb",
        "disableGeneHeuristic": true
      }
    },
    {
      "metadata": {
        "ucsc": {
          "track": "simpleRepeat",
          "shortLabel": "Simple Repeats",
          "longLabel": "Simple Tandem Repeats by TRF",
          "group": "varRep",
          "visibility": "dense",
          "type": "bigBed 4 +",
          "bigDataUrl": "bbi/GCF_025998455.1_ASM2599845v1.simpleRepeat.bb",
          "html": "<a href=\"https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/html/GCF_025998455.1_ASM2599845v1.simpleRepeat\">html/GCF_025998455.1_ASM2599845v1.simpleRepeat</a>"
        }
      },
      "category": ["Variation and Repeats"],
      "trackId": "GCF_025998455.1-simpleRepeat",
      "description": "Simple Tandem Repeats by TRF",
      "assemblyNames": ["GCF_025998455.1"],
      "name": "Simple Repeats",
      "type": "FeatureTrack",
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/bbi/GCF_025998455.1_ASM2599845v1.simpleRepeat.bb"
      }
    },
    {
      "metadata": {
        "ucsc": {
          "track": "ncbiGene",
          "longLabel": "Gene models submitted to GenBank, ENA, DDBJ",
          "shortLabel": "NCBI GenBank",
          "visibility": "pack",
          "color": "0,80,150",
          "altColor": "150,80,0",
          "colorByStrand": "0,80,150 150,80,0",
          "bigDataUrl": "bbi/GCF_025998455.1_ASM2599845v1.ncbiGene.bb",
          "type": "bigGenePred",
          "urls": "name2=\"https://www.ncbi.nlm.nih.gov/gene/?term=$$\" geneName=\"https://www.ncbi.nlm.nih.gov/gene/$$\" geneName2=\"https://www.ncbi.nlm.nih.gov/nuccore/$$\"",
          "html": "<a href=\"https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/html/GCF_025998455.1_ASM2599845v1.ncbiGene\">html/GCF_025998455.1_ASM2599845v1.ncbiGene</a>",
          "searchIndex": "name",
          "searchTrix": "ixIxx/GCF_025998455.1_ASM2599845v1.ncbiGene.ix",
          "urlLabel": "Entrez gene:",
          "labelFields": "geneName,geneName2",
          "defaultLabelFields": "geneName2",
          "group": "genes"
        }
      },
      "category": ["Genes and Gene Predictions"],
      "trackId": "GCF_025998455.1-ncbiGene",
      "description": "Gene models submitted to GenBank, ENA, DDBJ",
      "assemblyNames": ["GCF_025998455.1"],
      "name": "NCBI GenBank",
      "type": "FeatureTrack",
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/bbi/GCF_025998455.1_ASM2599845v1.ncbiGene.bb",
        "aggregateField": "geneName2"
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "GCF_025998455.1-ncbiGene-LinearBasicDisplay",
          "labels": {
            "name": "jexl:get(feature,'name')"
          }
        }
      ]
    },
    {
      "metadata": {
        "ucsc": {
          "track": "cpgIslandExt",
          "parent": "cpgIslands off",
          "shortLabel": "CpG Islands",
          "longLabel": "CpG Islands (Islands < 300 Bases are Light Green)",
          "type": "bigBed 4 +",
          "priority": "1",
          "bigDataUrl": "bbi/GCF_025998455.1_ASM2599845v1.cpgIslandExt.bb"
        }
      },
      "category": ["Regulation"],
      "trackId": "GCF_025998455.1-cpgIslandExt",
      "description": "CpG Islands (Islands < 300 Bases are Light Green)",
      "assemblyNames": ["GCF_025998455.1"],
      "name": "CpG Islands",
      "type": "FeatureTrack",
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/bbi/GCF_025998455.1_ASM2599845v1.cpgIslandExt.bb"
      }
    },
    {
      "metadata": {
        "ucsc": {
          "track": "cpgIslandExtUnmasked",
          "parent": "cpgIslands on",
          "shortLabel": "Unmasked CpG",
          "longLabel": "CpG Islands on All Sequence (Islands < 300 Bases are Light Green)",
          "type": "bigBed 4 +",
          "priority": "2",
          "bigDataUrl": "bbi/GCF_025998455.1_ASM2599845v1.cpgIslandExtUnmasked.bb"
        }
      },
      "category": ["Regulation"],
      "trackId": "GCF_025998455.1-cpgIslandExtUnmasked",
      "description": "CpG Islands on All Sequence (Islands < 300 Bases are Light Green)",
      "assemblyNames": ["GCF_025998455.1"],
      "name": "CpG Islands - Unmasked CpG",
      "type": "FeatureTrack",
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/bbi/GCF_025998455.1_ASM2599845v1.cpgIslandExtUnmasked.bb"
      }
    },
    {
      "metadata": {
        "ucsc": {
          "track": "windowMasker",
          "shortLabel": "WM + SDust",
          "longLabel": "Genomic Intervals Masked by WindowMasker + SDust",
          "group": "varRep",
          "visibility": "dense",
          "type": "bigBed 3",
          "bigDataUrl": "bbi/GCF_025998455.1_ASM2599845v1.windowMasker.bb",
          "html": "<a href=\"https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/html/GCF_025998455.1_ASM2599845v1.windowMasker\">html/GCF_025998455.1_ASM2599845v1.windowMasker</a>"
        }
      },
      "category": ["Variation and Repeats"],
      "trackId": "GCF_025998455.1-windowMasker",
      "description": "Genomic Intervals Masked by WindowMasker + SDust",
      "assemblyNames": ["GCF_025998455.1"],
      "name": "WM + SDust",
      "type": "FeatureTrack",
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://hgdownload.soe.ucsc.edu/hubs/GCF/025/998/455/GCF_025998455.1/bbi/GCF_025998455.1_ASM2599845v1.windowMasker.bb"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "GCF_025998455.1-ncbiGff",
      "name": "NCBI RefSeq - RefSeq All (GFF)",
      "adapter": {
        "type": "Gff3TabixAdapter",
        "gffGzLocation": {
          "uri": "GCF_025998455.1_ASM2599845v1_genomic.gff.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "GCF_025998455.1_ASM2599845v1_genomic.gff.gz.csi",
            "locationType": "UriLocation"
          },
          "indexType": "CSI"
        }
      },
      "category": ["Genes and Gene Predictions"],
      "assemblyNames": ["GCF_025998455.1"],
      "metadata": {
        "annotationDate": "2025-12-09",
        "annotationSource": "NCBI RefSeq GCF_025998455.1-RS_2025_12_09"
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "GCF_025998455.1-ncbiGff-LinearBasicDisplay",
          "labels": {
            "name": "jexl:get(feature,'standard_name')||get(feature,'name')||get(feature,'gene')||get(feature,'note')||get(feature,'function')||get(feature,'regulatory_class')||split(get(feature,'target')||'',' ')[0]"
          },
          "mouseover": "jexl:get(feature,'standard_name')||get(feature,'name')||get(feature,'gene')||get(feature,'note')||get(feature,'function')||get(feature,'regulatory_class')||split(get(feature,'target')||'',' ')[0]"
        }
      ],
      "textSearching": {
        "indexingAttributes": ["Name", "ID", "gene_synonym"],
        "indexingFeatureTypesToExclude": [
          "CDS",
          "exon",
          "region",
          "match",
          "cDNA_match",
          "biological_region",
          "enhancer",
          "silencer",
          "promoter",
          "protein_binding_site",
          "transcriptional_cis_regulatory_region",
          "nucleotide_motif"
        ]
      }
    }
  ],
  "defaultSession": {
    "name": "GCF_025998455.1",
    "widgets": {
      "hierarchicalTrackSelector": {
        "id": "hierarchicalTrackSelector",
        "type": "HierarchicalTrackSelectorWidget",
        "view": "initialView"
      }
    },
    "activeWidgets": {
      "hierarchicalTrackSelector": "hierarchicalTrackSelector"
    },
    "views": [
      {
        "type": "LinearGenomeView",
        "id": "initialView",
        "init": {
          "assembly": "GCF_025998455.1",
          "loc": "NZ_AP026446.1:565533-575533"
        }
      }
    ]
  },
  "aggregateTextSearchAdapters": [
    {
      "type": "TrixTextSearchAdapter",
      "textSearchAdapterId": "GCF_025998455.1-index",
      "ixFilePath": {
        "uri": "trix/GCF_025998455.1.ix",
        "locationType": "UriLocation"
      },
      "ixxFilePath": {
        "uri": "trix/GCF_025998455.1.ixx",
        "locationType": "UriLocation"
      },
      "metaFilePath": {
        "uri": "trix/GCF_025998455.1_meta.json",
        "locationType": "UriLocation"
      },
      "assemblyNames": ["GCF_025998455.1"]
    }
  ],
  "plugins": [
    {
      "name": "MafViewer",
      "url": "https://jbrowse.org/plugins/jbrowse-plugin-mafviewer/latest/dist/jbrowse-plugin-mafviewer.umd.production.min.js"
    },
    {
      "name": "Hubs",
      "storePlugin": "Hubs",
      "url": "https://jbrowse.org/plugins/@cmdcolin/jbrowse-plugin-hubs/latest/dist/jbrowse-plugin-hubs.umd.production.min.js"
    },
    {
      "name": "Protein3d",
      "storePlugin": "Protein3d",
      "url": "https://jbrowse.org/plugins/jbrowse-plugin-protein3d/latest/dist/jbrowse-plugin-protein3d.umd.production.min.js"
    },
    {
      "name": "MsaView",
      "storePlugin": "MsaView",
      "url": "https://jbrowse.org/plugins/jbrowse-plugin-msaview/latest/dist/jbrowse-plugin-msaview.umd.production.min.js"
    }
  ],
  "configuration": {
    "hierarchical": {
      "sort": {
        "trackNames": true,
        "categories": true
      },
      "defaultCollapsed": {
        "topLevelCategories": true,
        "subCategories": true
      }
    }
  }
}
