diff test-data/samtools_stats_out2/sn.tab @ 0:cd6eb75c9819 draft

Uploaded initial tool definition.
author devteam
date Mon, 20 Oct 2014 14:56:49 -0400
parents
children cc56fc603e53
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/samtools_stats_out2/sn.tab	Mon Oct 20 14:56:49 2014 -0400
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+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