Mercurial > repos > devteam > samtools_stats

comparison test-data/11.stats.expected @ 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 e28839a4b932
children
comparison
equal deleted inserted replaced
11:fed4aa48ba09 12:541082d03bef
1 # This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats 1 # This file was produced by samtools stats (1.20+htslib-1.20) and can be plotted using plot-bamstats
2 # This file contains statistics for all reads. 2 # This file contains statistics for all reads.
3 # The command line was: stats -@ 0 infile ref1:10-24 ref1:30-46 ref1:39-56 3 # The command line was: stats -@ 0 infile ref1:10-24 ref1:30-46 ref1:39-56
4 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities 4 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities
5 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) 5 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
6 CHK cb2d2d82 bcd83869 62ec814e 6 CHK cb2d2d82 bcd83869 62ec814e
181 RL 10 26 181 RL 10 26
182 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count 182 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count
183 FRL 10 14 183 FRL 10 14
184 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count 184 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count
185 LRL 10 12 185 LRL 10 12
186 # Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count
187 MAPQ 0 1
188 MAPQ 1 1
189 MAPQ 2 1
190 MAPQ 3 1
191 MAPQ 4 1
192 MAPQ 5 1
193 MAPQ 6 1
194 MAPQ 7 1
195 MAPQ 8 1
196 MAPQ 9 1
197 MAPQ 10 1
198 MAPQ 11 1
199 MAPQ 12 1
200 MAPQ 13 1
201 MAPQ 14 1
202 MAPQ 15 1
203 MAPQ 16 1
204 MAPQ 17 1
205 MAPQ 18 1
206 MAPQ 19 1
207 MAPQ 20 1
208 MAPQ 21 1
209 MAPQ 22 1
210 MAPQ 23 1
211 MAPQ 50 2
186 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions 212 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions
187 # Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev) 213 # Indels per cycle. Use `grep ^IC | cut -f 2-` to extract this part. The columns are: cycle, number of insertions (fwd), .. (rev) , number of deletions (fwd), .. (rev)
188 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. 214 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.
189 COV [1-1] 1 1 215 COV [1-1] 1 1
190 COV [2-2] 2 1 216 COV [2-2] 2 1