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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit cd62639660bef041ba14ecff337fb98e84e75d8a
| author | iuc |
|---|---|
| date | Mon, 20 Nov 2023 22:17:08 +0000 |
| parents | e28839a4b932 |
| children | 541082d03bef |
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# This file was produced by samtools stats (1.12+htslib-1.12) and can be plotted using plot-bamstats # This file contains statistics for all reads. # The command line was: stats -g 4 -@ 0 infile ref1:10-24 ref1:30-46 ref1:39-56 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow) CHK cb2d2d82 bcd83869 62ec814e # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part. SN raw total sequences: 26 # excluding supplementary and secondary reads SN filtered sequences: 0 SN sequences: 26 SN is sorted: 1 SN 1st fragments: 14 SN last fragments: 12 SN reads mapped: 26 SN reads mapped and paired: 26 # paired-end technology bit set + both mates mapped SN reads unmapped: 0 SN reads properly paired: 24 # proper-pair bit set SN reads paired: 26 # paired-end technology bit set SN reads duplicated: 0 # PCR or optical duplicate bit set SN reads MQ0: 1 # mapped and MQ=0 SN reads QC failed: 0 SN non-primary alignments: 0 SN supplementary alignments: 0 SN total length: 260 # ignores clipping SN total first fragment length: 140 # ignores clipping SN total last fragment length: 120 # ignores clipping SN bases mapped: 260 # ignores clipping SN bases mapped (cigar): 206 # 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: 10 SN average first fragment length: 10 SN average last fragment length: 10 SN maximum length: 10 SN maximum first fragment length: 10 SN maximum last fragment length: 10 SN average quality: 13.1 SN insert size average: 34.0 SN insert size standard deviation: 0.0 SN inward oriented pairs: 12 SN outward oriented pairs: 0 SN pairs with other orientation: 0 SN pairs on different chromosomes: 1 SN percentage of properly paired reads (%): 92.3 SN bases inside the target: 42 SN percentage of target genome with coverage > 4 (%): 85.71 # 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. FFQ 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 FFQ 2 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 FFQ 3 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 FFQ 4 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 FFQ 5 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 FFQ 6 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 FFQ 7 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 FFQ 8 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 FFQ 9 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 FFQ 10 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 # Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part. # Columns correspond to qualities and rows to cycles. First column is the cycle number. LFQ 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 LFQ 2 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 LFQ 3 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 LFQ 4 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 LFQ 5 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 LFQ 6 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 LFQ 7 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 LFQ 8 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 LFQ 9 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 0 0 0 0 0 0 0 0 0 0 LFQ 10 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 1 1 1 1 1 1 1 1 1 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 19.85 0 GCF 44.72 1 GCF 54.77 4 GCF 64.82 2 GCF 74.87 4 GCF 84.92 3 # GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part. GCL 19.85 0 GCL 44.72 2 GCL 59.80 3 GCL 74.87 4 # 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 19.23 42.31 15.38 23.08 0.00 0.00 GCC 2 19.23 19.23 46.15 15.38 0.00 0.00 GCC 3 23.08 38.46 19.23 19.23 0.00 0.00 GCC 4 23.08 23.08 38.46 15.38 0.00 0.00 GCC 5 11.54 38.46 26.92 23.08 0.00 0.00 GCC 6 23.08 23.08 34.62 19.23 0.00 0.00 GCC 7 15.38 34.62 26.92 23.08 0.00 0.00 GCC 8 26.92 23.08 38.46 11.54 0.00 0.00 GCC 9 23.08 26.92 26.92 23.08 0.00 0.00 GCC 10 23.08 23.08 38.46 15.38 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 26.92 26.92 30.77 15.38 GCT 2 7.69 38.46 26.92 26.92 GCT 3 26.92 26.92 30.77 15.38 GCT 4 11.54 34.62 26.92 26.92 GCT 5 23.08 26.92 38.46 11.54 GCT 6 11.54 34.62 23.08 30.77 GCT 7 19.23 23.08 38.46 19.23 GCT 8 11.54 38.46 23.08 26.92 GCT 9 23.08 19.23 34.62 23.08 GCT 10 11.54 34.62 26.92 26.92 # 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 [%] FBC 1 21.43 42.86 21.43 14.29 0.00 0.00 FBC 2 7.14 28.57 42.86 21.43 0.00 0.00 FBC 3 28.57 35.71 21.43 14.29 0.00 0.00 FBC 4 14.29 28.57 35.71 21.43 0.00 0.00 FBC 5 14.29 35.71 35.71 14.29 0.00 0.00 FBC 6 14.29 28.57 28.57 28.57 0.00 0.00 FBC 7 14.29 28.57 35.71 21.43 0.00 0.00 FBC 8 21.43 28.57 28.57 21.43 0.00 0.00 FBC 9 21.43 21.43 35.71 21.43 0.00 0.00 FBC 10 14.29 28.57 35.71 21.43 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 24 43 45 28 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 16.67 41.67 8.33 33.33 0.00 0.00 LBC 2 33.33 8.33 50.00 8.33 0.00 0.00 LBC 3 16.67 41.67 16.67 25.00 0.00 0.00 LBC 4 33.33 16.67 41.67 8.33 0.00 0.00 LBC 5 8.33 41.67 16.67 33.33 0.00 0.00 LBC 6 33.33 16.67 41.67 8.33 0.00 0.00 LBC 7 16.67 41.67 16.67 25.00 0.00 0.00 LBC 8 33.33 16.67 50.00 0.00 0.00 0.00 LBC 9 25.00 33.33 16.67 25.00 0.00 0.00 LBC 10 33.33 16.67 41.67 8.33 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 30 33 36 21 0 # 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 [%] BCC1 1 50.00 0.00 0.00 50.00 0.00 BCC1 2 0.00 50.00 50.00 0.00 0.00 BCC1 3 0.00 50.00 50.00 0.00 0.00 BCC1 4 50.00 0.00 0.00 50.00 0.00 # Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part. # Columns correspond to qualities and rows to barcode cycles. First column is the cycle number. QTQ1 1 QTQ1 2 QTQ1 3 QTQ1 4 # 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 12 12 0 0 # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count RL 10 26 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count FRL 10 14 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count LRL 10 12 # 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 1 COV [2-2] 2 1 COV [3-3] 3 2 COV [4-4] 4 2 COV [5-5] 5 23 COV [6-6] 6 13 # 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