Mercurial > repos > matthias > bam_to_sam
comparison samtools_stats/test-data/samtools_stats_out2__sn.tab @ 0:56e8f02cf63a draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
| author | matthias |
|---|---|
| date | Fri, 22 Feb 2019 15:40:36 -0500 |
| parents | |
| children |
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| -1:000000000000 | 0:56e8f02cf63a |
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| 1 # Summary Numbers | |
| 2 | |
| 3 raw total sequences: 200 | |
| 4 filtered sequences: 0 | |
| 5 sequences: 200 | |
| 6 is sorted: 1 | |
| 7 1st fragments: 100 | |
| 8 last fragments: 100 | |
| 9 reads mapped: 25 | |
| 10 reads mapped and paired: 0 # paired-end technology bit set + both mates mapped | |
| 11 reads unmapped: 175 | |
| 12 reads properly paired: 0 # proper-pair bit set | |
| 13 reads paired: 200 # paired-end technology bit set | |
| 14 reads duplicated: 0 # PCR or optical duplicate bit set | |
| 15 reads MQ0: 6 # mapped and MQ=0 | |
| 16 reads QC failed: 0 | |
| 17 non-primary alignments: 0 | |
| 18 total length: 50200 # ignores clipping | |
| 19 bases mapped: 6275 # ignores clipping | |
| 20 bases mapped (cigar): 6275 # more accurate | |
| 21 bases trimmed: 0 | |
| 22 bases duplicated: 0 | |
| 23 mismatches: 591 # from NM fields | |
| 24 error rate: 9.418327e-02 # mismatches / bases mapped (cigar) | |
| 25 average length: 251 | |
| 26 maximum length: 251 | |
| 27 average quality: 34.7 | |
| 28 insert size average: 0.0 | |
| 29 insert size standard deviation: 0.0 | |
| 30 inward oriented pairs: 0 | |
| 31 outward oriented pairs: 0 | |
| 32 pairs with other orientation: 0 | |
| 33 pairs on different chromosomes: 0 |