View Single Post
Old 07-31-2017, 03:51 PM   #1
charon
Junior Member
 
Location: houston

Join Date: Feb 2013
Posts: 2
Default 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!
charon is offline   Reply With Quote