Mercurial > repos > devteam > samtools_stats
comparison test-data/11.stats.expected @ 8:e28839a4b932 draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 0f75269223c0821c6c82acf98fde947d0f816f2b"
| author | iuc |
|---|---|
| date | Tue, 28 Sep 2021 16:17:39 +0000 |
| parents | 95a7ddf617e7 |
| children | 541082d03bef |
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| 7:145f6d74ff5e | 8:e28839a4b932 |
|---|---|
| 1 # This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats | |
| 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 | |
| 1 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities | 4 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities |
| 2 # 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) |
| 3 CHK cb2d2d82 bcd83869 62ec814e | 6 CHK cb2d2d82 bcd83869 62ec814e |
| 4 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. | 7 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. |
| 5 SN raw total sequences: 26 | 8 SN raw total sequences: 26 # excluding supplementary and secondary reads |
| 6 SN filtered sequences: 0 | 9 SN filtered sequences: 0 |
| 7 SN sequences: 26 | 10 SN sequences: 26 |
| 8 SN is sorted: 1 | 11 SN is sorted: 1 |
| 9 SN 1st fragments: 14 | 12 SN 1st fragments: 14 |
| 10 SN last fragments: 12 | 13 SN last fragments: 12 |
| 15 SN reads paired: 26 # paired-end technology bit set | 18 SN reads paired: 26 # paired-end technology bit set |
| 16 SN reads duplicated: 0 # PCR or optical duplicate bit set | 19 SN reads duplicated: 0 # PCR or optical duplicate bit set |
| 17 SN reads MQ0: 1 # mapped and MQ=0 | 20 SN reads MQ0: 1 # mapped and MQ=0 |
| 18 SN reads QC failed: 0 | 21 SN reads QC failed: 0 |
| 19 SN non-primary alignments: 0 | 22 SN non-primary alignments: 0 |
| 23 SN supplementary alignments: 0 | |
| 20 SN total length: 260 # ignores clipping | 24 SN total length: 260 # ignores clipping |
| 21 SN total first fragment length: 140 # ignores clipping | 25 SN total first fragment length: 140 # ignores clipping |
| 22 SN total last fragment length: 120 # ignores clipping | 26 SN total last fragment length: 120 # ignores clipping |
| 23 SN bases mapped: 260 # ignores clipping | 27 SN bases mapped: 260 # ignores clipping |
| 24 SN bases mapped (cigar): 206 # more accurate | 28 SN bases mapped (cigar): 206 # more accurate |
| 87 GCC 6 23.08 23.08 34.62 19.23 0.00 0.00 | 91 GCC 6 23.08 23.08 34.62 19.23 0.00 0.00 |
| 88 GCC 7 15.38 34.62 26.92 23.08 0.00 0.00 | 92 GCC 7 15.38 34.62 26.92 23.08 0.00 0.00 |
| 89 GCC 8 26.92 23.08 38.46 11.54 0.00 0.00 | 93 GCC 8 26.92 23.08 38.46 11.54 0.00 0.00 |
| 90 GCC 9 23.08 26.92 26.92 23.08 0.00 0.00 | 94 GCC 9 23.08 26.92 26.92 23.08 0.00 0.00 |
| 91 GCC 10 23.08 23.08 38.46 15.38 0.00 0.00 | 95 GCC 10 23.08 23.08 38.46 15.38 0.00 0.00 |
| 96 # 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 [%] | |
| 97 GCT 1 26.92 26.92 30.77 15.38 | |
| 98 GCT 2 7.69 38.46 26.92 26.92 | |
| 99 GCT 3 26.92 26.92 30.77 15.38 | |
| 100 GCT 4 11.54 34.62 26.92 26.92 | |
| 101 GCT 5 23.08 26.92 38.46 11.54 | |
| 102 GCT 6 11.54 34.62 23.08 30.77 | |
| 103 GCT 7 19.23 23.08 38.46 19.23 | |
| 104 GCT 8 11.54 38.46 23.08 26.92 | |
| 105 GCT 9 23.08 19.23 34.62 23.08 | |
| 106 GCT 10 11.54 34.62 26.92 26.92 | |
| 92 # 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 [%] | 107 # 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 [%] |
| 93 FBC 1 21.43 42.86 21.43 14.29 0.00 0.00 | 108 FBC 1 21.43 42.86 21.43 14.29 0.00 0.00 |
| 94 FBC 2 7.14 28.57 42.86 21.43 0.00 0.00 | 109 FBC 2 7.14 28.57 42.86 21.43 0.00 0.00 |
| 95 FBC 3 28.57 35.71 21.43 14.29 0.00 0.00 | 110 FBC 3 28.57 35.71 21.43 14.29 0.00 0.00 |
| 96 FBC 4 14.29 28.57 35.71 21.43 0.00 0.00 | 111 FBC 4 14.29 28.57 35.71 21.43 0.00 0.00 |
| 98 FBC 6 14.29 28.57 28.57 28.57 0.00 0.00 | 113 FBC 6 14.29 28.57 28.57 28.57 0.00 0.00 |
| 99 FBC 7 14.29 28.57 35.71 21.43 0.00 0.00 | 114 FBC 7 14.29 28.57 35.71 21.43 0.00 0.00 |
| 100 FBC 8 21.43 28.57 28.57 21.43 0.00 0.00 | 115 FBC 8 21.43 28.57 28.57 21.43 0.00 0.00 |
| 101 FBC 9 21.43 21.43 35.71 21.43 0.00 0.00 | 116 FBC 9 21.43 21.43 35.71 21.43 0.00 0.00 |
| 102 FBC 10 14.29 28.57 35.71 21.43 0.00 0.00 | 117 FBC 10 14.29 28.57 35.71 21.43 0.00 0.00 |
| 118 # 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 | |
| 119 FTC 24 43 45 28 0 | |
| 103 # 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 [%] | 120 # 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 [%] |
| 104 LBC 1 16.67 41.67 8.33 33.33 0.00 0.00 | 121 LBC 1 16.67 41.67 8.33 33.33 0.00 0.00 |
| 105 LBC 2 33.33 8.33 50.00 8.33 0.00 0.00 | 122 LBC 2 33.33 8.33 50.00 8.33 0.00 0.00 |
| 106 LBC 3 16.67 41.67 16.67 25.00 0.00 0.00 | 123 LBC 3 16.67 41.67 16.67 25.00 0.00 0.00 |
| 107 LBC 4 33.33 16.67 41.67 8.33 0.00 0.00 | 124 LBC 4 33.33 16.67 41.67 8.33 0.00 0.00 |
| 109 LBC 6 33.33 16.67 41.67 8.33 0.00 0.00 | 126 LBC 6 33.33 16.67 41.67 8.33 0.00 0.00 |
| 110 LBC 7 16.67 41.67 16.67 25.00 0.00 0.00 | 127 LBC 7 16.67 41.67 16.67 25.00 0.00 0.00 |
| 111 LBC 8 33.33 16.67 50.00 0.00 0.00 0.00 | 128 LBC 8 33.33 16.67 50.00 0.00 0.00 0.00 |
| 112 LBC 9 25.00 33.33 16.67 25.00 0.00 0.00 | 129 LBC 9 25.00 33.33 16.67 25.00 0.00 0.00 |
| 113 LBC 10 33.33 16.67 41.67 8.33 0.00 0.00 | 130 LBC 10 33.33 16.67 41.67 8.33 0.00 0.00 |
| 131 # 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 | |
| 132 LTC 30 33 36 21 0 | |
| 133 # ACGT content per cycle for barcodes. Use `grep ^BCC | 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 counts as a percentage of all A/C/G/T bases [%] | |
| 134 BCC1 1 50.00 0.00 0.00 50.00 0.00 | |
| 135 BCC1 2 0.00 50.00 50.00 0.00 0.00 | |
| 136 BCC1 3 0.00 50.00 50.00 0.00 0.00 | |
| 137 BCC1 4 50.00 0.00 0.00 50.00 0.00 | |
| 138 # Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part. | |
| 139 # Columns correspond to qualities and rows to barcode cycles. First column is the cycle number. | |
| 140 QTQ1 1 | |
| 141 QTQ1 2 | |
| 142 QTQ1 3 | |
| 143 QTQ1 4 | |
| 114 # 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 | 144 # 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 |
| 115 IS 0 0 0 0 0 | 145 IS 0 0 0 0 0 |
| 116 IS 1 0 0 0 0 | 146 IS 1 0 0 0 0 |
| 117 IS 2 0 0 0 0 | 147 IS 2 0 0 0 0 |
| 118 IS 3 0 0 0 0 | 148 IS 3 0 0 0 0 |