Feature Coverage Tracks

Introduced in JBrowse 1.7.0, feature coverage tracks show a dynamically-computed XY-plot of the depth of coverage of features across a genome. One good use of this track type is to provide a quick coverage plot directly from a BAM file. However, since this track calculates coverage on the fly, it can be very slow when used with large regions or very deep coverage. In this case, it is recommended to generate a BigWig file containing the coverage data, and display it with a Wiggle/XYPlot or Wiggle/Density track.

Feature coverage tracks are a special type of Wiggle/XYPlot tracks, so the same configuration options apply. There is an additional caveat, however: this kind of track requires the min_score and max_score variables in order to set the Y-axis scaling, since these cannot be quickly determined from raw BAM or other feature data.

Note: The SNPCoverage track and FeatureCoverage tracks are very similar, except the SNPCoverage track (in addition to showing SNPs) also has the extra ability to filter the supplementary/secondary reads, and other reads, so they may appear to report different coverages by default.

Example Feature Coverage Track Configuration for a BAM file

      {
         "storeClass"  :  "JBrowse/Store/SeqFeature/BAM",
         "urlTemplate" : "../../raw/volvox/volvox-sorted.bam",
         "label"       : "volvox-sorted.bam_coverage",
         "type"        : "JBrowse/View/Track/FeatureCoverage",
         "min_score"   : 0,
         "max_score"   : 35,
         "key"         : "volvox-sorted Coverage"
      }