Mercurial > repos > devteam > samtools_stats
view test-data/2.stats.expected @ 12:541082d03bef draft default tip
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 |
line wrap: on
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# This file was produced by samtools stats (1.20+htslib-1.20) and can be plotted using plot-bamstats # This file contains statistics for all reads. # The command line was: stats --ref-seq reference.fa -@ 0 infile # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK 1a1c1362 29c426ae 7bab45da # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. SN raw total sequences: 2 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 2 SN is sorted: 1 SN 1st fragments: 1 SN last fragments: 1 SN reads mapped: 2 SN reads mapped and paired: 2 # paired-end technology bit set + both mates mapped SN reads unmapped: 0 SN reads properly paired: 2 # proper-pair bit set SN reads paired: 2 # paired-end technology bit set SN reads duplicated: 0 # PCR or optical duplicate bit set SN reads MQ0: 0 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 SN supplementary alignments: 0 SN total length: 70 # ignores clipping SN total first fragment length: 35 # ignores clipping SN total last fragment length: 35 # ignores clipping SN bases mapped: 70 # ignores clipping SN bases mapped (cigar): 70 # more accurate SN bases trimmed: 0 SN bases duplicated: 0 SN mismatches: 0 # from NM fields SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar) SN average length: 35 SN average first fragment length: 35 SN average last fragment length: 35 SN maximum length: 35 SN maximum first fragment length: 35 SN maximum last fragment length: 35 SN average quality: 255.0 SN insert size average: 100.0 SN insert size standard deviation: 0.0 SN inward oriented pairs: 1 SN outward oriented pairs: 0 SN pairs with other orientation: 0 SN pairs on different chromosomes: 0 SN percentage of properly paired reads (%): 100.0 # First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part. # Columns correspond to qualities and rows to cycles. First column is the cycle number. 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0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 MPC 36 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 # GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part. GCF 28.39 0 GCF 58.29 1 # GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. GCL 21.36 0 GCL 43.97 1 # ACGT content per cycle. Use `grep ^GCC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] GCC 1 0.00 0.00 50.00 50.00 0.00 0.00 GCC 2 0.00 0.00 50.00 50.00 0.00 0.00 GCC 3 50.00 0.00 50.00 0.00 0.00 0.00 GCC 4 0.00 50.00 50.00 0.00 0.00 0.00 GCC 5 50.00 0.00 50.00 0.00 0.00 0.00 GCC 6 0.00 0.00 50.00 50.00 0.00 0.00 GCC 7 50.00 0.00 50.00 0.00 0.00 0.00 GCC 8 50.00 0.00 0.00 50.00 0.00 0.00 GCC 9 0.00 100.00 0.00 0.00 0.00 0.00 GCC 10 50.00 50.00 0.00 0.00 0.00 0.00 GCC 11 0.00 0.00 0.00 100.00 0.00 0.00 GCC 12 50.00 50.00 0.00 0.00 0.00 0.00 GCC 13 0.00 0.00 50.00 50.00 0.00 0.00 GCC 14 50.00 0.00 0.00 50.00 0.00 0.00 GCC 15 50.00 0.00 0.00 50.00 0.00 0.00 GCC 16 100.00 0.00 0.00 0.00 0.00 0.00 GCC 17 0.00 50.00 0.00 50.00 0.00 0.00 GCC 18 0.00 100.00 0.00 0.00 0.00 0.00 GCC 19 0.00 50.00 50.00 0.00 0.00 0.00 GCC 20 50.00 0.00 50.00 0.00 0.00 0.00 GCC 21 0.00 50.00 50.00 0.00 0.00 0.00 GCC 22 0.00 0.00 50.00 50.00 0.00 0.00 GCC 23 0.00 0.00 0.00 100.00 0.00 0.00 GCC 24 0.00 0.00 50.00 50.00 0.00 0.00 GCC 25 0.00 0.00 50.00 50.00 0.00 0.00 GCC 26 0.00 50.00 50.00 0.00 0.00 0.00 GCC 27 100.00 0.00 0.00 0.00 0.00 0.00 GCC 28 50.00 0.00 50.00 0.00 0.00 0.00 GCC 29 0.00 0.00 50.00 50.00 0.00 0.00 GCC 30 50.00 50.00 0.00 0.00 0.00 0.00 GCC 31 0.00 100.00 0.00 0.00 0.00 0.00 GCC 32 0.00 50.00 50.00 0.00 0.00 0.00 GCC 33 50.00 0.00 0.00 50.00 0.00 0.00 GCC 34 50.00 0.00 50.00 0.00 0.00 0.00 GCC 35 0.00 0.00 50.00 50.00 0.00 0.00 # ACGT content per cycle, read oriented. Use `grep ^GCT | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%] GCT 1 0.00 50.00 0.00 50.00 GCT 2 50.00 0.00 50.00 0.00 GCT 3 0.00 0.00 50.00 50.00 GCT 4 0.00 0.00 100.00 0.00 GCT 5 0.00 0.00 50.00 50.00 GCT 6 0.00 50.00 0.00 50.00 GCT 7 0.00 0.00 50.00 50.00 GCT 8 0.00 0.00 0.00 100.00 GCT 9 0.00 50.00 50.00 0.00 GCT 10 50.00 0.00 50.00 0.00 GCT 11 50.00 0.00 0.00 50.00 GCT 12 50.00 0.00 50.00 0.00 GCT 13 50.00 0.00 50.00 0.00 GCT 14 0.00 0.00 0.00 100.00 GCT 15 100.00 0.00 0.00 0.00 GCT 16 50.00 0.00 0.00 50.00 GCT 17 0.00 0.00 50.00 50.00 GCT 18 0.00 50.00 50.00 0.00 GCT 19 0.00 100.00 0.00 0.00 GCT 20 0.00 0.00 50.00 50.00 GCT 21 0.00 0.00 100.00 0.00 GCT 22 0.00 50.00 0.00 50.00 GCT 23 50.00 0.00 0.00 50.00 GCT 24 50.00 0.00 50.00 0.00 GCT 25 50.00 0.00 50.00 0.00 GCT 26 0.00 0.00 100.00 0.00 GCT 27 50.00 0.00 0.00 50.00 GCT 28 0.00 0.00 50.00 50.00 GCT 29 0.00 50.00 0.00 50.00 GCT 30 0.00 50.00 0.00 50.00 GCT 31 0.00 50.00 50.00 0.00 GCT 32 0.00 0.00 100.00 0.00 GCT 33 100.00 0.00 0.00 0.00 GCT 34 0.00 0.00 50.00 50.00 GCT 35 50.00 0.00 50.00 0.00 # ACGT content per cycle for first fragments. Use `grep ^FBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 FBC 3 0.00 0.00 100.00 0.00 0.00 0.00 FBC 4 0.00 0.00 100.00 0.00 0.00 0.00 FBC 5 0.00 0.00 100.00 0.00 0.00 0.00 FBC 6 0.00 0.00 0.00 100.00 0.00 0.00 FBC 7 0.00 0.00 100.00 0.00 0.00 0.00 FBC 8 0.00 0.00 0.00 100.00 0.00 0.00 FBC 9 0.00 100.00 0.00 0.00 0.00 0.00 FBC 10 100.00 0.00 0.00 0.00 0.00 0.00 FBC 11 0.00 0.00 0.00 100.00 0.00 0.00 FBC 12 100.00 0.00 0.00 0.00 0.00 0.00 FBC 13 0.00 0.00 100.00 0.00 0.00 0.00 FBC 14 0.00 0.00 0.00 100.00 0.00 0.00 FBC 15 100.00 0.00 0.00 0.00 0.00 0.00 FBC 16 100.00 0.00 0.00 0.00 0.00 0.00 FBC 17 0.00 0.00 0.00 100.00 0.00 0.00 FBC 18 0.00 100.00 0.00 0.00 0.00 0.00 FBC 19 0.00 100.00 0.00 0.00 0.00 0.00 FBC 20 0.00 0.00 100.00 0.00 0.00 0.00 FBC 21 0.00 0.00 100.00 0.00 0.00 0.00 FBC 22 0.00 0.00 0.00 100.00 0.00 0.00 FBC 23 0.00 0.00 0.00 100.00 0.00 0.00 FBC 24 0.00 0.00 100.00 0.00 0.00 0.00 FBC 25 0.00 0.00 100.00 0.00 0.00 0.00 FBC 26 0.00 0.00 100.00 0.00 0.00 0.00 FBC 27 100.00 0.00 0.00 0.00 0.00 0.00 FBC 28 0.00 0.00 100.00 0.00 0.00 0.00 FBC 29 0.00 0.00 0.00 100.00 0.00 0.00 FBC 30 0.00 100.00 0.00 0.00 0.00 0.00 FBC 31 0.00 100.00 0.00 0.00 0.00 0.00 FBC 32 0.00 0.00 100.00 0.00 0.00 0.00 FBC 33 100.00 0.00 0.00 0.00 0.00 0.00 FBC 34 0.00 0.00 100.00 0.00 0.00 0.00 FBC 35 0.00 0.00 100.00 0.00 0.00 0.00 # ACGT raw counters for first fragments. Use `grep ^FTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters FTC 6 5 15 9 0 # ACGT content per cycle for last fragments. Use `grep ^LBC | cut -f 2-` to extract this part. The columns are: cycle; A,C,G,T base counts as a percentage of all A/C/G/T bases [%]; and N and O counts as a percentage of all A/C/G/T bases [%] LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 LBC 2 0.00 0.00 0.00 100.00 0.00 0.00 LBC 3 100.00 0.00 0.00 0.00 0.00 0.00 LBC 4 0.00 100.00 0.00 0.00 0.00 0.00 LBC 5 100.00 0.00 0.00 0.00 0.00 0.00 LBC 6 0.00 0.00 100.00 0.00 0.00 0.00 LBC 7 100.00 0.00 0.00 0.00 0.00 0.00 LBC 8 100.00 0.00 0.00 0.00 0.00 0.00 LBC 9 0.00 100.00 0.00 0.00 0.00 0.00 LBC 10 0.00 100.00 0.00 0.00 0.00 0.00 LBC 11 0.00 0.00 0.00 100.00 0.00 0.00 LBC 12 0.00 100.00 0.00 0.00 0.00 0.00 LBC 13 0.00 0.00 0.00 100.00 0.00 0.00 LBC 14 100.00 0.00 0.00 0.00 0.00 0.00 LBC 15 0.00 0.00 0.00 100.00 0.00 0.00 LBC 16 100.00 0.00 0.00 0.00 0.00 0.00 LBC 17 0.00 100.00 0.00 0.00 0.00 0.00 LBC 18 0.00 100.00 0.00 0.00 0.00 0.00 LBC 19 0.00 0.00 100.00 0.00 0.00 0.00 LBC 20 100.00 0.00 0.00 0.00 0.00 0.00 LBC 21 0.00 100.00 0.00 0.00 0.00 0.00 LBC 22 0.00 0.00 100.00 0.00 0.00 0.00 LBC 23 0.00 0.00 0.00 100.00 0.00 0.00 LBC 24 0.00 0.00 0.00 100.00 0.00 0.00 LBC 25 0.00 0.00 0.00 100.00 0.00 0.00 LBC 26 0.00 100.00 0.00 0.00 0.00 0.00 LBC 27 100.00 0.00 0.00 0.00 0.00 0.00 LBC 28 100.00 0.00 0.00 0.00 0.00 0.00 LBC 29 0.00 0.00 100.00 0.00 0.00 0.00 LBC 30 100.00 0.00 0.00 0.00 0.00 0.00 LBC 31 0.00 100.00 0.00 0.00 0.00 0.00 LBC 32 0.00 100.00 0.00 0.00 0.00 0.00 LBC 33 0.00 0.00 0.00 100.00 0.00 0.00 LBC 34 100.00 0.00 0.00 0.00 0.00 0.00 LBC 35 0.00 0.00 0.00 100.00 0.00 0.00 # ACGT raw counters for last fragments. Use `grep ^LTC | cut -f 2-` to extract this part. The columns are: A,C,G,T,N base counters LTC 11 10 5 9 0 # Insert sizes. Use `grep ^IS | cut -f 2-` to extract this part. The columns are: insert size, pairs total, inward oriented pairs, outward oriented pairs, other pairs IS 0 0 0 0 0 IS 1 0 0 0 0 IS 2 0 0 0 0 IS 3 0 0 0 0 IS 4 0 0 0 0 IS 5 0 0 0 0 IS 6 0 0 0 0 IS 7 0 0 0 0 IS 8 0 0 0 0 IS 9 0 0 0 0 IS 10 0 0 0 0 IS 11 0 0 0 0 IS 12 0 0 0 0 IS 13 0 0 0 0 IS 14 0 0 0 0 IS 15 0 0 0 0 IS 16 0 0 0 0 IS 17 0 0 0 0 IS 18 0 0 0 0 IS 19 0 0 0 0 IS 20 0 0 0 0 IS 21 0 0 0 0 IS 22 0 0 0 0 IS 23 0 0 0 0 IS 24 0 0 0 0 IS 25 0 0 0 0 IS 26 0 0 0 0 IS 27 0 0 0 0 IS 28 0 0 0 0 IS 29 0 0 0 0 IS 30 0 0 0 0 IS 31 0 0 0 0 IS 32 0 0 0 0 IS 33 0 0 0 0 IS 34 0 0 0 0 IS 35 0 0 0 0 IS 36 0 0 0 0 IS 37 0 0 0 0 IS 38 0 0 0 0 IS 39 0 0 0 0 IS 40 0 0 0 0 IS 41 0 0 0 0 IS 42 0 0 0 0 IS 43 0 0 0 0 IS 44 0 0 0 0 IS 45 0 0 0 0 IS 46 0 0 0 0 IS 47 0 0 0 0 IS 48 0 0 0 0 IS 49 0 0 0 0 IS 50 0 0 0 0 IS 51 0 0 0 0 IS 52 0 0 0 0 IS 53 0 0 0 0 IS 54 0 0 0 0 IS 55 0 0 0 0 IS 56 0 0 0 0 IS 57 0 0 0 0 IS 58 0 0 0 0 IS 59 0 0 0 0 IS 60 0 0 0 0 IS 61 0 0 0 0 IS 62 0 0 0 0 IS 63 0 0 0 0 IS 64 0 0 0 0 IS 65 0 0 0 0 IS 66 0 0 0 0 IS 67 0 0 0 0 IS 68 0 0 0 0 IS 69 0 0 0 0 IS 70 0 0 0 0 IS 71 0 0 0 0 IS 72 0 0 0 0 IS 73 0 0 0 0 IS 74 0 0 0 0 IS 75 0 0 0 0 IS 76 0 0 0 0 IS 77 0 0 0 0 IS 78 0 0 0 0 IS 79 0 0 0 0 IS 80 0 0 0 0 IS 81 0 0 0 0 IS 82 0 0 0 0 IS 83 0 0 0 0 IS 84 0 0 0 0 IS 85 0 0 0 0 IS 86 0 0 0 0 IS 87 0 0 0 0 IS 88 0 0 0 0 IS 89 0 0 0 0 IS 90 0 0 0 0 IS 91 0 0 0 0 IS 92 0 0 0 0 IS 93 0 0 0 0 IS 94 0 0 0 0 IS 95 0 0 0 0 IS 96 0 0 0 0 IS 97 0 0 0 0 IS 98 0 0 0 0 IS 99 0 0 0 0 IS 100 1 1 0 0 # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count RL 35 2 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count FRL 35 1 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count LRL 35 1 # Mapping qualities for reads !(UNMAP|SECOND|SUPPL|QCFAIL|DUP). Use `grep ^MAPQ | cut -f 2-` to extract this part. The columns are: mapq, count MAPQ 40 2 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions # 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) # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part. COV [1-1] 1 70 # 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 GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000