raw total sequences:	1000
filtered sequences:	0
sequences:	1000
is sorted:	1
1st fragments:	500
last fragments:	500
reads mapped:	972
reads mapped and paired:	954	# paired-end technology bit set + both mates mapped
reads unmapped:	28
reads properly paired:	0	# proper-pair bit set
reads paired:	1000	# paired-end technology bit set
reads duplicated:	0	# PCR or optical duplicate bit set
reads MQ0:	0	# mapped and MQ=0
reads QC failed:	0
non-primary alignments:	0
total length:	70000	# ignores clipping
bases mapped:	68040	# ignores clipping
bases mapped (cigar):	68040	# more accurate
bases trimmed:	0
bases duplicated:	0
mismatches:	1237	# from NM fields
error rate:	1.818048e-02	# mismatches / bases mapped (cigar)
average length:	70
maximum length:	70
average quality:	17.0
insert size average:	495.1
insert size standard deviation:	48.9
inward oriented pairs:	477
outward oriented pairs:	0
pairs with other orientation:	0
pairs on different chromosomes:	0