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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit f10a2b16814f61326750364c497ad143cac3d137-dirty
author matthias
date Mon, 25 Feb 2019 03:53:00 -0500
parents 8f08fd44a749
children
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8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
1 # Summary Numbers
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
2
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
3 raw total sequences: 200
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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4 filtered sequences: 0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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5 sequences: 200
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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6 is sorted: 1
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
7 1st fragments: 100
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
8 last fragments: 100
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
9 reads mapped: 25
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
10 reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
11 reads unmapped: 175
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
12 reads properly paired: 0 # proper-pair bit set
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
13 reads paired: 200 # paired-end technology bit set
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
14 reads duplicated: 0 # PCR or optical duplicate bit set
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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15 reads MQ0: 6 # mapped and MQ=0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
16 reads QC failed: 0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
17 non-primary alignments: 0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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18 total length: 50200 # ignores clipping
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
19 bases mapped: 6275 # ignores clipping
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
20 bases mapped (cigar): 6275 # more accurate
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
21 bases trimmed: 0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
22 bases duplicated: 0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
23 mismatches: 591 # from NM fields
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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24 error rate: 9.418327e-02 # mismatches / bases mapped (cigar)
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
25 average length: 251
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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26 maximum length: 251
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
27 average quality: 34.7
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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28 insert size average: 0.0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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29 insert size standard deviation: 0.0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
30 inward oriented pairs: 0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
31 outward oriented pairs: 0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
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32 pairs with other orientation: 0
8f08fd44a749 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
33 pairs on different chromosomes: 0