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annotate test-data/samtools_stats_out2__sn.tab @ 3:45c568e7f1f9 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
author iuc
date Tue, 09 May 2017 11:17:02 -0400
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45c568e7f1f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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diff changeset
1 # Summary Numbers
45c568e7f1f9 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
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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
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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
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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
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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
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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
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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
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diff changeset
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
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diff changeset
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
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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
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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
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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
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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
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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
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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
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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
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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:
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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
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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:
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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
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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
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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
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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
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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
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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
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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
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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:
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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
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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
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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
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33 pairs on different chromosomes: 0