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annotate test-data/samtools_stats_out1__sn.tab @ 4:8d500e0e0dbe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
author iuc
date Thu, 27 Sep 2018 08:59:54 -0400
parents
children ab75c7ea49a5
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4
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
1 # Summary Numbers.
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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diff changeset
2 raw total sequences: 200
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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3 filtered sequences: 0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
4 sequences: 200
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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diff changeset
5 is sorted: 1
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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6 1st fragments: 100
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
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7 last fragments: 100
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
8 reads mapped: 25
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
9 reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
10 reads unmapped: 175
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
11 reads properly paired: 0 # proper-pair bit set
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
12 reads paired: 200 # paired-end technology bit set
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
13 reads duplicated: 0 # PCR or optical duplicate bit set
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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14 reads MQ0: 6 # mapped and MQ=0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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diff changeset
15 reads QC failed: 0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
16 non-primary alignments: 0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
17 total length: 50200 # ignores clipping
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
18 total first fragment length: 25100 # ignores clipping
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
19 total last fragment length: 25100 # ignores clipping
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
20 bases mapped: 6275 # ignores clipping
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
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21 bases mapped (cigar): 6275 # more accurate
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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22 bases trimmed: 0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
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23 bases duplicated: 0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
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24 mismatches: 591 # from NM fields
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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25 error rate: 9.418327e-02 # mismatches / bases mapped (cigar)
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
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26 average length: 251
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
27 average first fragment length: 251
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
28 average last fragment length: 251
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
29 maximum length: 251
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
30 maximum first fragment length: 251
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
diff changeset
31 maximum last fragment length: 251
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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32 average quality: 34.7
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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33 insert size average: 0.0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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34 insert size standard deviation: 0.0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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35 inward oriented pairs: 0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
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36 outward oriented pairs: 0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
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37 pairs with other orientation: 0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
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38 pairs on different chromosomes: 0
8d500e0e0dbe planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
iuc
parents:
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39 percentage of properly paired reads (%): 0.0