Mercurial > repos > devteam > samtools_stats

# Summary Numbers

raw total sequences:	200
filtered sequences:	0
sequences:	200
is sorted:	1
1st fragments:	100
last fragments:	100
reads mapped:	25
reads mapped and paired:	0	# paired-end technology bit set + both mates mapped
reads unmapped:	175
reads properly paired:	0	# proper-pair bit set
reads paired:	200	# paired-end technology bit set
reads duplicated:	0	# PCR or optical duplicate bit set
reads MQ0:	6	# mapped and MQ=0
reads QC failed:	0
non-primary alignments:	0
total length:	50200	# ignores clipping
bases mapped:	6275	# ignores clipping
bases mapped (cigar):	6275	# more accurate
bases trimmed:	0
bases duplicated:	0
mismatches:	591	# from NM fields
error rate:	9.418327e-02	# mismatches / bases mapped (cigar)
average length:	251
maximum length:	251
average quality:	34.7
insert size average:	0.0
insert size standard deviation:	0.0
inward oriented pairs:	0
outward oriented pairs:	0
pairs with other orientation:	0
pairs on different chromosomes:	0
author	devteam
date	Tue, 13 Oct 2015 12:56:27 -0400
parents	cd6eb75c9819
children