{
  "assemblies": [
    {
      "name": "hg002v1.2",
      "displayName": "T2T-HG002 v1.2 (diploid)",
      "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/hg002v1.2.fasta.gz"
    }
  ],
  "tracks": [
    {
      "type": "SyntenyTrack",
      "trackId": "hg002v1.2_mat_vs_pat",
      "name": "Maternal vs paternal (Q100 chain)",
      "assemblyNames": ["hg002v1.2", "hg002v1.2"],
      "adapter": {
        "type": "ChainAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/changes/hg002v1.2_to_other_haplotype.chain.gz",
        "queryAssembly": "hg002v1.2",
        "targetAssembly": "hg002v1.2"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg002v1.2_hetsites",
      "name": "Heterozygous sites",
      "assemblyNames": ["hg002v1.2"],
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/annotation/haplotypes/v1.2.hetsites.bb"
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg002v1.2_chainblocks_mat",
      "name": "Chain blocks (maternal)",
      "assemblyNames": ["hg002v1.2"],
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/annotation/browserchains/hg002v1.2.mat2pat.bigChain.bb"
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "hg002v1.2_chainblocks_mat-LinearBasicDisplay",
          "showLabels": "none",
          "color": { "field": "strand" }
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg002v1.2_chainblocks_pat",
      "name": "Chain blocks (paternal)",
      "assemblyNames": ["hg002v1.2"],
      "adapter": {
        "type": "BigBedAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/annotation/browserchains/hg002v1.2.pat2mat.bigChain.bb"
      },
      "displays": [
        {
          "type": "LinearBasicDisplay",
          "displayId": "hg002v1.2_chainblocks_pat-LinearBasicDisplay",
          "showLabels": "none",
          "color": { "field": "strand" }
        }
      ]
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg002_genes_mat",
      "name": "Genes (JHU Liftoff v0.6, HG002 v1.1 MAT)",
      "assemblyNames": ["hg002v1.2"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/annotation/JHULiftoff/v0.6/hg002v1.1.MAT.loff.v0.6.gff.gz"
      },
      "displayDefaults": {
        "geneGlyphMode": "longestCoding",
        "labels": {
          "name": "jexl:feature.gene_name || feature.name || feature.id"
        },
        "color": { "field": "strand" }
      }
    },
    {
      "type": "FeatureTrack",
      "trackId": "hg002_genes_pat",
      "name": "Genes (JHU Liftoff v0.6, HG002 v1.1 PAT)",
      "assemblyNames": ["hg002v1.2"],
      "adapter": {
        "type": "Gff3TabixAdapter",
        "uri": "https://s3-us-west-2.amazonaws.com/human-pangenomics/T2T/HG002/assemblies/annotation/JHULiftoff/v0.6/hg002v1.1.PAT.loff.v0.6.gff.gz"
      },
      "displayDefaults": {
        "geneGlyphMode": "longestCoding",
        "labels": {
          "name": "jexl:feature.gene_name || feature.name || feature.id"
        },
        "color": { "field": "strand" }
      }
    }
  ]
}
