{
   "tracks" : [
      {
         "label" : "DNA",
         "key" : "Reference sequence",
         "seqType" : "dna",
         "category" : "Reference sequence",
         "storeClass" : "JBrowse/Store/Sequence/StaticChunked",
         "urlTemplate" : "seq/{refseq_dirpath}/{refseq}-",
         "chunkSize" : 20000,
         "type" : "SequenceTrack"
      },
      {
         "type" : "MAFViewer/View/Track/MAF",
         "samples" : [
            "ce10",
            "cb4",
            "caeRem4",
            "caePb3",
            "caeSp111",
            "caeJap4"
         ],
         "storeClass" : "MAFViewer/Store/SeqFeature/MAFTabix",
         "urlTemplate" : "chrI.txt.gz",
         "label" : "MAF"
      },
      {
         "samples" : [
            "cb4",
            "caeRem4",
            "caePb3",
            "caeSp111",
            "caeJap4"
         ],
         "type" : "MAFViewer/View/Track/MAF",
         "style" : {
            "height" : 40
         },
         "storeClass" : "MAFViewer/Store/SeqFeature/MAF",
         "urlTemplate" : "chrI.txt.gz",
         "label" : "MAF modheight"
      },
      {
         "label" : "MAF bases",
         "urlTemplate" : "chrI.txt.gz",
         "storeClass" : "MAFViewer/Store/SeqFeature/MAF",
         "style" : {
            "mismatchBases" : true,
            "mismatchA": "blue",
            "mismatchC": "red",
            "mismatchG": "orange",
            "mismatchT": "yellow"
         },
         "type" : "MAFViewer/View/Track/MAF",
         "samples" : [
            "cb4",
            "caeRem4",
            "caePb3",
            "caeSp111",
            "caeJap4"
         ]
      },
      {
         "label" : "MAF modcolor",
         "urlTemplate" : "chrI.txt.gz",
         "storeClass" : "MAFViewer/Store/SeqFeature/MAF",
         "style" : {
            "mismatchColor" : "orange",
            "matchColor" : "blue"
         },
         "type" : "MAFViewer/View/Track/MAF",
         "samples" : [
            "cb4",
            "caeRem4",
            "caePb3",
            "caeSp111",
            "caeJap4"
         ]
      },
      {
         "label" : "MAF CF",
         "type" : "CanvasFeatures",
         "urlTemplate" : "chrI.txt.gz",
         "storeClass" : "JBrowse/Store/SeqFeature/BEDTabix"
      },
      {
         "label" : "augustusGene",
         "key" : "augustusGene",
         "hooks" : {
            "modify" : "function(track, feat, elem) {\n    var fType = feat.get(\"Type\");\n    if (fType) {\n        elem.className = \"basic\";\n        switch (fType) {\n        case \"CDS\":\n        case \"thick\":\n            elem.style.height = \"10px\";\n            elem.style.marginTop = \"-3px\";\n            break;\n        case \"UTR\":\n        case \"thin\":\n            elem.style.height = \"6px\";\n            elem.style.marginTop = \"-1px\";\n            break;\n        }\n        elem.style.backgroundColor = \"#0c6900\";\n    }\n}\n"
         },
         "compress" : 0,
         "style" : {
            "className" : "generic_parent",
            "histCss" : "background-color: #0c6900;",
            "featureCss" : "background-color: #0c6900; height: 6px;"
         },
         "storeClass" : "JBrowse/Store/SeqFeature/NCList",
         "urlTemplate" : "tracks/augustusGene/{refseq}/trackData.json",
         "type" : "FeatureTrack"
      }
   ],
   "plugins" : [
      "MAFViewer",
      "HideTrackLabels"
   ],
   "classicMenu" : true,
   "formatVersion" : 1,
   "highResolutionMode": 2
}
