Mercurial > repos > devteam > samtools_stats
comparison test-data/1.stats.expected @ 12:8fecc86e574a draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 9c5a35ce695c3d134e41d8695487edd5f71ea33c
author | iuc |
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date | Sun, 08 Sep 2024 03:23:56 +0000 |
parents | ab75c7ea49a5 |
children |
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11:a95f78faca04 | 12:8fecc86e574a |
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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 --ref-seq reference.fa -@ 0 infile | 3 # The command line was: stats --ref-seq reference.fa -@ 0 infile |
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 1a1c1362 29c426ae 7bab45da | 6 CHK 1a1c1362 29c426ae 7bab45da |
417 RL 35 2 | 417 RL 35 2 |
418 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count | 418 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count |
419 FRL 35 1 | 419 FRL 35 1 |
420 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count | 420 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count |
421 LRL 35 1 | 421 LRL 35 1 |
422 # Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count | |
423 MAPQ 40 2 | |
422 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions | 424 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions |
423 # 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) | 425 # 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) |
424 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. | 426 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. |
425 COV [1-1] 1 70 | 427 COV [1-1] 1 70 |
426 # GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile | 428 # GC-depth. Use `grep ^GCD | cut -f 2-` to extract this part. The columns are: GC%, unique sequence percentiles, 10th, 25th, 50th, 75th and 90th depth percentile |