Mercurial > repos > devteam > samtools_stats
diff test-data/samtools_stats_out2/sn.tab @ 0:cd6eb75c9819 draft
Uploaded initial tool definition.
author | devteam |
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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 @@ -0,0 +1,31 @@ +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