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  • what does "average quality" mean in samtools stat

    I used samtools stats to measure some basic metrics of a input bam file and got the following results:


    raw total sequences: 1105415
    filtered sequences: 80516
    sequences: 1024899
    is sorted: 1
    1st fragments: 1024899
    last fragments: 0
    reads mapped: 940001
    reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
    reads unmapped: 84898
    reads properly paired: 0 # proper-pair bit set
    reads paired: 0 # paired-end technology bit set
    reads duplicated: 0 # PCR or optical duplicate bit set
    reads MQ0: 14800 # mapped and MQ=0
    reads QC failed: 0
    non-primary alignments: 0
    total length: 5395194643 # ignores clipping
    bases mapped: 4998712634 # ignores clipping
    bases mapped (cigar): 4531562523 # more accurate
    bases trimmed: 0
    bases duplicated: 0
    mismatches: 688215582 # from NM fields
    error rate: 1.518716e-01 # mismatches / bases mapped (cigar)
    average quality: 19.8
    insert size average: 0.0

    How was wondering how's the average quality calculated? (It's a bit higher than I expected) Is it related to read's mean base quality? i.e. For each read, calculate its mean base quality, and then take the average of all reads?

    Thanks in advance!

  • #2
    The base qualities for the whole file are summed and then that's divided by the total number of bases in the file.

    Comment


    • #3
      Makes sense. Thanks dpryan!

      Comment

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