Mercurial > repos > devteam > samtools_stats

annotate test-data/samtools_stats_out2__sn.tab @ 12:541082d03bef draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author iuc
date Sun, 08 Sep 2024 03:27:04 +0000
parents 24c5d43cb545
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
2
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
1 # Summary Numbers
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
2
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
3 raw total sequences: 200
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
4 filtered sequences: 0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
5 sequences: 200
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
6 is sorted: 1
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
7 1st fragments: 100
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
8 last fragments: 100
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
9 reads mapped: 25
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
10 reads mapped and paired: 0 # paired-end technology bit set + both mates mapped
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
11 reads unmapped: 175
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
12 reads properly paired: 0 # proper-pair bit set
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
13 reads paired: 200 # paired-end technology bit set
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
14 reads duplicated: 0 # PCR or optical duplicate bit set
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
15 reads MQ0: 6 # mapped and MQ=0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
16 reads QC failed: 0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
17 non-primary alignments: 0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
18 total length: 50200 # ignores clipping
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
19 bases mapped: 6275 # ignores clipping
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
20 bases mapped (cigar): 6275 # more accurate
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
21 bases trimmed: 0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
22 bases duplicated: 0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
23 mismatches: 591 # from NM fields
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
24 error rate: 9.418327e-02 # mismatches / bases mapped (cigar)
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
25 average length: 251
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
26 maximum length: 251
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
27 average quality: 34.7
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
28 insert size average: 0.0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
29 insert size standard deviation: 0.0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
30 inward oriented pairs: 0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
31 outward oriented pairs: 0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
32 pairs with other orientation: 0
24c5d43cb545 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 411130b45dc30f7f24f41cdeec5e148c5d8faf40
iuc
parents:
diff changeset
33 pairs on different chromosomes: 0