Mercurial > repos > devteam > samtools_stats
annotate test-data/samtools_stats_out2__sn.tab @ 8:df598009c821 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 95fe80d08fb14c4c344da4979290e72261e31ae5"
author | iuc |
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date | Thu, 10 Oct 2019 03:39:57 -0400 |
parents | 45c568e7f1f9 |
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rev | line source |
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3
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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1 # Summary Numbers |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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2 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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3 raw total sequences: 200 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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4 filtered sequences: 0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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5 sequences: 200 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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6 is sorted: 1 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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7 1st fragments: 100 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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8 last fragments: 100 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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9 reads mapped: 25 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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10 reads mapped and paired: 0 # paired-end technology bit set + both mates mapped |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
11 reads unmapped: 175 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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12 reads properly paired: 0 # proper-pair bit set |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
13 reads paired: 200 # paired-end technology bit set |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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14 reads duplicated: 0 # PCR or optical duplicate bit set |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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15 reads MQ0: 6 # mapped and MQ=0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
16 reads QC failed: 0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
17 non-primary alignments: 0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
18 total length: 50200 # ignores clipping |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
19 bases mapped: 6275 # ignores clipping |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
20 bases mapped (cigar): 6275 # more accurate |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
21 bases trimmed: 0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
22 bases duplicated: 0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
23 mismatches: 591 # from NM fields |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
24 error rate: 9.418327e-02 # mismatches / bases mapped (cigar) |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
25 average length: 251 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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26 maximum length: 251 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
27 average quality: 34.7 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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28 insert size average: 0.0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
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29 insert size standard deviation: 0.0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
30 inward oriented pairs: 0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
31 outward oriented pairs: 0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
32 pairs with other orientation: 0 |
45c568e7f1f9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff
changeset
|
33 pairs on different chromosomes: 0 |