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comparison 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
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children ab75c7ea49a5
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3:45c568e7f1f9 4:8d500e0e0dbe
1 # Summary Numbers.
2 raw total sequences: 200
3 filtered sequences: 0
4 sequences: 200
5 is sorted: 1
6 1st fragments: 100
7 last fragments: 100
8 reads mapped: 25
9 reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
10 reads unmapped: 175
11 reads properly paired: 0 # proper-pair bit set
12 reads paired: 200 # paired-end technology bit set
13 reads duplicated: 0 # PCR or optical duplicate bit set
14 reads MQ0: 6 # mapped and MQ=0
15 reads QC failed: 0
16 non-primary alignments: 0
17 total length: 50200 # ignores clipping
18 total first fragment length: 25100 # ignores clipping
19 total last fragment length: 25100 # ignores clipping
20 bases mapped: 6275 # ignores clipping
21 bases mapped (cigar): 6275 # more accurate
22 bases trimmed: 0
23 bases duplicated: 0
24 mismatches: 591 # from NM fields
25 error rate: 9.418327e-02 # mismatches / bases mapped (cigar)
26 average length: 251
27 average first fragment length: 251
28 average last fragment length: 251
29 maximum length: 251
30 maximum first fragment length: 251
31 maximum last fragment length: 251
32 average quality: 34.7
33 insert size average: 0.0
34 insert size standard deviation: 0.0
35 inward oriented pairs: 0
36 outward oriented pairs: 0
37 pairs with other orientation: 0
38 pairs on different chromosomes: 0
39 percentage of properly paired reads (%): 0.0