view samtools_stats/test-data/samtools_stats_out1__sn.tab @ 0:fe46361a85db draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty

# 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
total first fragment length:	25100	# ignores clipping
total last fragment length:	25100	# 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
average first fragment length:	251
average last fragment length:	251
maximum length:	251
maximum first fragment length:	251
maximum last fragment 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
percentage of properly paired reads (%):	0.0