Mercurial > repos > devteam > samtools_stats
diff test-data/samtools_stats_out2/sn.tab @ 1:cc56fc603e53 draft
planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
| author | devteam |
|---|---|
| date | Tue, 13 Oct 2015 12:56:27 -0400 |
| parents | cd6eb75c9819 |
| children |
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--- a/test-data/samtools_stats_out2/sn.tab Mon Oct 20 14:56:49 2014 -0400 +++ b/test-data/samtools_stats_out2/sn.tab Tue Oct 13 12:56:27 2015 -0400 @@ -1,31 +1,33 @@ -raw total sequences: 1000 +# Summary Numbers + +raw total sequences: 200 filtered sequences: 0 -sequences: 1000 +sequences: 200 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 +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: 1000 # paired-end technology bit set +reads paired: 200 # paired-end technology bit set reads duplicated: 0 # PCR or optical duplicate bit set -reads MQ0: 0 # mapped and MQ=0 +reads MQ0: 6 # 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 +total length: 50200 # ignores clipping +bases mapped: 6275 # ignores clipping +bases mapped (cigar): 6275 # 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 +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
