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annotate samtools_stats/test-data/samtools_stats_out1__sn.tab @ 0:6c9caf40b95e draft

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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 15:42:15 -0500
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6c9caf40b95e 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.
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
2 raw total sequences: 200
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
3 filtered sequences: 0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
4 sequences: 200
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
5 is sorted: 1
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
6 1st fragments: 100
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
7 last fragments: 100
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
8 reads mapped: 25
6c9caf40b95e 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 and paired: 0 # paired-end technology bit set + both mates mapped
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
10 reads unmapped: 175
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
11 reads properly paired: 0 # proper-pair bit set
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
12 reads paired: 200 # paired-end technology bit set
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
13 reads duplicated: 0 # PCR or optical duplicate bit set
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
14 reads MQ0: 6 # mapped and MQ=0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
15 reads QC failed: 0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
16 non-primary alignments: 0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
17 total length: 50200 # ignores clipping
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
18 total first fragment length: 25100 # ignores clipping
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
19 total last fragment length: 25100 # ignores clipping
6c9caf40b95e 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: 6275 # ignores clipping
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
21 bases mapped (cigar): 6275 # more accurate
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
22 bases trimmed: 0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
23 bases duplicated: 0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
24 mismatches: 591 # from NM fields
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
25 error rate: 9.418327e-02 # mismatches / bases mapped (cigar)
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
26 average length: 251
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
27 average first fragment length: 251
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
28 average last fragment length: 251
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
29 maximum length: 251
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
30 maximum first fragment length: 251
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
31 maximum last fragment length: 251
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
32 average quality: 34.7
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
33 insert size average: 0.0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
34 insert size standard deviation: 0.0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
35 inward oriented pairs: 0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
36 outward oriented pairs: 0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
37 pairs with other orientation: 0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
38 pairs on different chromosomes: 0
6c9caf40b95e planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools commit 17bfa0739bf7c72cf92de0d7013437dff2bbba7f-dirty
matthias
parents:
diff changeset
39 percentage of properly paired reads (%): 0.0