Coverage per contig

[Joanna Hård]

In the genome_results.txt output file, there is one section labeled:

>>>>>>> Coverage per contig

        1       249250621       1817570229      7.292139219986136       130.94559410681435

        2       243199373       2429749279      9.990771148081866       1062.2861372815764

        3       198022430       1631796394      8.240462426402908       230.07737393041666

        4       191154276       1644507625      8.603038652402418       178.53599385019749

etc...

The first column 1-4 etc, are chromosomes I assume. What are the four remaining columns with data?

[Konstantin Okonechnikov]

Hi!

These columns show the same values as in graphical HTML/PDF report per chromosome/reference: name, sequence length, sum of total mapped bases, coverage mean and  standard deviation.

Here's an example information:

http://kokonech.github.io/qualimap/HG00096.chr20_bamqc/qualimapReport.html#summary

Best regards,

   Konstantin

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