{
  "assemblies": [
    {
      "name": "mm10",
      "aliases": ["GRCm38"],
      "sequence": {
        "type": "ReferenceSequenceTrack",
        "trackId": "mm10-ReferenceSequenceTrack",
        "adapter": {
          "type": "BgzipFastaAdapter",
          "uri": "https://jbrowse.org/genomes/mm10/fasta/mm10.fa.gz"
        }
      },
      "refNameAliases": {
        "adapter": {
          "type": "RefNameAliasAdapter",
          "uri": "https://hgdownload.soe.ucsc.edu/goldenpath/mm10/bigZips/latest/mm10.chromAlias.txt"
        }
      },
      "cytobands": {
        "adapter": {
          "type": "CytobandAdapter",
          "uri": "https://jbrowse.org/ucsc/mm10/cytoBandIdeo.bed.gz"
        }
      }
    }
  ],
  "tracks": [
    {
      "type": "FeatureTrack",
      "trackId": "mm10_ncbi_refseq",
      "name": "NCBI RefSeq genes (mm10)",
      "assemblyNames": ["mm10"],
      "category": ["Genes"],
      "adapter": {
        "type": "GtfTabixAdapter",
        "gtfGzLocation": {
          "uri": "https://jbrowse.org/demos/bxd/mm10.ncbiRefSeq.sorted.gtf.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/bxd/mm10.ncbiRefSeq.sorted.gtf.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "bxd_chromosome_painting_mm10",
      "name": "BXD chromosome painting (GeneNetwork, 198 strains)",
      "assemblyNames": ["mm10"],
      "category": ["GeneNetwork / BXD"],
      "adapter": {
        "type": "BedTabixAdapter",
        "disableGeneHeuristic": true,
        "bedGzLocation": {
          "uri": "https://jbrowse.org/demos/bxd/bxd_painting.bed.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/bxd/bxd_painting.bed.gz.tbi",
            "locationType": "UriLocation"
          }
        }
      },
      "displays": [
        {
          "type": "LinearMultiRowFeatureDisplay",
          "displayId": "bxd_chromosome_painting_mm10-LinearMultiRowFeatureDisplay",
          "rows": "sample",
          "color": {
            "scale": "identity",
            "domain": ["rgb(65,105,225)", "rgb(220,60,50)", "rgb(150,150,150)"],
            "labels": ["B (C57BL/6J)", "D (DBA/2J)", "H (heterozygous)"],
            "title": "Genotype"
          },
          "height": 700,
          "rowGroups": [
            {
              "match": "^(BXD100|BXD105|BXD109|BXD11|BXD110|BXD116|BXD119|BXD120|BXD121|BXD123|BXD124|BXD125|BXD128a|BXD131|BXD133|BXD136|BXD14|BXD142|BXD145|BXD148|BXD149|BXD151|BXD152|BXD153|BXD154|BXD156|BXD165|BXD171|BXD173|BXD186|BXD190|BXD191|BXD199|BXD2|BXD20|BXD204|BXD207|BXD210|BXD217|BXD218|BXD219|BXD23|BXD31|BXD32|BXD34|BXD35|BXD42|BXD43|BXD48|BXD48a|BXD50|BXD51|BXD56|BXD86|BXD87)$",
              "group": "black"
            },
            {
              "match": "^(BXD101|BXD117|BXD12|BXD122|BXD130|BXD135|BXD139|BXD141|BXD144|BXD146|BXD147|BXD155|BXD157|BXD16|BXD162|BXD169|BXD172|BXD174|BXD175|BXD176|BXD178|BXD18|BXD180|BXD181|BXD183|BXD184|BXD19|BXD198|BXD202|BXD205|BXD208|BXD211|BXD212|BXD215|BXD22|BXD29|BXD33|BXD38|BXD39|BXD40|BXD49|BXD5|BXD6|BXD76|BXD79|BXD8|BXD94)$",
              "group": "grey"
            },
            {
              "match": "^(BXD102|BXD104|BXD106|BXD108|BXD111|BXD114|BXD115|BXD126|BXD127|BXD128|BXD13|BXD132|BXD134|BXD15|BXD150|BXD177|BXD192|BXD193|BXD194|BXD195|BXD196|BXD197|BXD200|BXD203|BXD209|BXD24|BXD24a|BXD25|BXD27|BXD28|BXD36|BXD52|BXD53|BXD55|BXD59|BXD60|BXD62|BXD65|BXD65a|BXD66|BXD68|BXD72|BXD74|BXD78|BXD88)$",
              "group": "brown"
            },
            {
              "match": "^(BXD1|BXD107|BXD112|BXD113|BXD138|BXD160|BXD161|BXD168|BXD170|BXD187|BXD188|BXD189|BXD201|BXD206|BXD21|BXD216|BXD220|BXD30|BXD44|BXD45|BXD61|BXD63|BXD64|BXD65b|BXD67|BXD69|BXD70|BXD71|BXD73|BXD73a|BXD73b|BXD75|BXD77|BXD81|BXD83|BXD84|BXD85|BXD89|BXD9|BXD90|BXD91|BXD93|BXD95|BXD98|BXD99)$",
              "group": "dilute brown"
            }
          ],
          "rowColor": {
            "field": "group",
            "domain": ["black", "grey", "brown", "dilute brown"],
            "range": [
              "rgb(30,30,30)",
              "rgb(150,150,160)",
              "rgb(130,80,40)",
              "rgb(210,175,130)"
            ]
          },
          "facet": "group"
        }
      ]
    },
    {
      "type": "GWASTrack",
      "trackId": "bxd_gwas_coatcolor_mm10",
      "name": "BXD QTL: coat color (GEMMA)",
      "assemblyNames": ["mm10"],
      "category": ["GeneNetwork / BXD"],
      "adapter": {
        "type": "GWASAdapter",
        "bedGzLocation": {
          "uri": "https://jbrowse.org/demos/bxd/bxd_gwas_coatcolor.tsv.gz",
          "locationType": "UriLocation"
        },
        "index": {
          "location": {
            "uri": "https://jbrowse.org/demos/bxd/bxd_gwas_coatcolor.tsv.gz.tbi",
            "locationType": "UriLocation"
          }
        },
        "scoreColumn": "lod"
      },
      "displays": [
        {
          "type": "LinearManhattanDisplay",
          "displayId": "bxd_gwas_coatcolor_mm10-LinearManhattanDisplay",
          "scales": {
            "y": {
              "title": "LOD"
            }
          }
        }
      ]
    }
  ],
  "defaultSession": {
    "name": "BXD systems genetics (GeneNetwork)",
    "views": [
      {
        "id": "bxd_lgv",
        "type": "LinearGenomeView",
        "assembly": "mm10",
        "loc": "chr4",
        "tracks": ["bxd_gwas_coatcolor_mm10", "bxd_chromosome_painting_mm10"]
      }
    ]
  }
}