Mercurial > repos > devteam > samtools_stats
comparison 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 |
comparison
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| -1:000000000000 | 0:cd6eb75c9819 |
|---|---|
| 1 raw total sequences: 1000 | |
| 2 filtered sequences: 0 | |
| 3 sequences: 1000 | |
| 4 is sorted: 1 | |
| 5 1st fragments: 500 | |
| 6 last fragments: 500 | |
| 7 reads mapped: 972 | |
| 8 reads mapped and paired: 954 # paired-end technology bit set + both mates mapped | |
| 9 reads unmapped: 28 | |
| 10 reads properly paired: 0 # proper-pair bit set | |
| 11 reads paired: 1000 # paired-end technology bit set | |
| 12 reads duplicated: 0 # PCR or optical duplicate bit set | |
| 13 reads MQ0: 0 # mapped and MQ=0 | |
| 14 reads QC failed: 0 | |
| 15 non-primary alignments: 0 | |
| 16 total length: 70000 # ignores clipping | |
| 17 bases mapped: 68040 # ignores clipping | |
| 18 bases mapped (cigar): 68040 # more accurate | |
| 19 bases trimmed: 0 | |
| 20 bases duplicated: 0 | |
| 21 mismatches: 1237 # from NM fields | |
| 22 error rate: 1.818048e-02 # mismatches / bases mapped (cigar) | |
| 23 average length: 70 | |
| 24 maximum length: 70 | |
| 25 average quality: 17.0 | |
| 26 insert size average: 495.1 | |
| 27 insert size standard deviation: 48.9 | |
| 28 inward oriented pairs: 477 | |
| 29 outward oriented pairs: 0 | |
| 30 pairs with other orientation: 0 | |
| 31 pairs on different chromosomes: 0 |