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comparison test-data/samtools_stats_out2__sn.tab @ 2:24c5d43cb545 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 11:19:01 -0400
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1:8cfc17e27132 2:24c5d43cb545
1 # Summary Numbers
2
3 raw total sequences: 200
4 filtered sequences: 0
5 sequences: 200
6 is sorted: 1
7 1st fragments: 100
8 last fragments: 100
9 reads mapped: 25
10 reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
11 reads unmapped: 175
12 reads properly paired: 0 # proper-pair bit set
13 reads paired: 200 # paired-end technology bit set
14 reads duplicated: 0 # PCR or optical duplicate bit set
15 reads MQ0: 6 # mapped and MQ=0
16 reads QC failed: 0
17 non-primary alignments: 0
18 total length: 50200 # ignores clipping
19 bases mapped: 6275 # ignores clipping
20 bases mapped (cigar): 6275 # more accurate
21 bases trimmed: 0
22 bases duplicated: 0
23 mismatches: 591 # from NM fields
24 error rate: 9.418327e-02 # mismatches / bases mapped (cigar)
25 average length: 251
26 maximum length: 251
27 average quality: 34.7
28 insert size average: 0.0
29 insert size standard deviation: 0.0
30 inward oriented pairs: 0
31 outward oriented pairs: 0
32 pairs with other orientation: 0
33 pairs on different chromosomes: 0