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comparison test-data/samtools_stats_out2/sn.tab @ 1:cc56fc603e53 draft

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planemo upload commit 33927a87ba2eee9bf0ecdd376a66241b17b3d734
author devteam
date Tue, 13 Oct 2015 12:56:27 -0400
parents cd6eb75c9819
children
comparison
equal deleted inserted replaced
0:cd6eb75c9819 1:cc56fc603e53
1 raw total sequences: 1000 1 # Summary Numbers
2
3 raw total sequences: 200
2 filtered sequences: 0 4 filtered sequences: 0
3 sequences: 1000 5 sequences: 200
4 is sorted: 1 6 is sorted: 1
5 1st fragments: 500 7 1st fragments: 100
6 last fragments: 500 8 last fragments: 100
7 reads mapped: 972 9 reads mapped: 25
8 reads mapped and paired: 954 # paired-end technology bit set + both mates mapped 10 reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
9 reads unmapped: 28 11 reads unmapped: 175
10 reads properly paired: 0 # proper-pair bit set 12 reads properly paired: 0 # proper-pair bit set
11 reads paired: 1000 # paired-end technology bit set 13 reads paired: 200 # paired-end technology bit set
12 reads duplicated: 0 # PCR or optical duplicate bit set 14 reads duplicated: 0 # PCR or optical duplicate bit set
13 reads MQ0: 0 # mapped and MQ=0 15 reads MQ0: 6 # mapped and MQ=0
14 reads QC failed: 0 16 reads QC failed: 0
15 non-primary alignments: 0 17 non-primary alignments: 0
16 total length: 70000 # ignores clipping 18 total length: 50200 # ignores clipping
17 bases mapped: 68040 # ignores clipping 19 bases mapped: 6275 # ignores clipping
18 bases mapped (cigar): 68040 # more accurate 20 bases mapped (cigar): 6275 # more accurate
19 bases trimmed: 0 21 bases trimmed: 0
20 bases duplicated: 0 22 bases duplicated: 0
21 mismatches: 1237 # from NM fields 23 mismatches: 591 # from NM fields
22 error rate: 1.818048e-02 # mismatches / bases mapped (cigar) 24 error rate: 9.418327e-02 # mismatches / bases mapped (cigar)
23 average length: 70 25 average length: 251
24 maximum length: 70 26 maximum length: 251
25 average quality: 17.0 27 average quality: 34.7
26 insert size average: 495.1 28 insert size average: 0.0
27 insert size standard deviation: 48.9 29 insert size standard deviation: 0.0
28 inward oriented pairs: 477 30 inward oriented pairs: 0
29 outward oriented pairs: 0 31 outward oriented pairs: 0
30 pairs with other orientation: 0 32 pairs with other orientation: 0
31 pairs on different chromosomes: 0 33 pairs on different chromosomes: 0