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To export a coverage of the assembly, select the Export coverage item in the Consensus Area context menu.

The Export Coverage dialog appears:

The following parameters are available:

  • Export to - select the result file path,
  • Format - assembly coverage could be saved in three different formats:
    • Bedgraph - the coverage shown by columns. If several columns in a row have the same occurrence, they will be joint into one column.
    • Histogram - shows coverage by frequency of occurrence. That is, a row is deciphered as a column number N with coverage X occurs in an assembly of a length L and the total occurrence rate is Z:

    • Per base - similar to BaseGraph, but without columns merging.
      • Export coverage value - add coverage for each base (how many reads in the column).
      • Export bases quantity - add the amount of A, C, G and T.
  • Threshold - consider the column only if it has more reads than set by this parameter.
  • Compress the file - archive as .gz.

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