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comparison test-data/11.stats.g4.expected @ 8:e28839a4b932 draft

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"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
comparison
equal deleted inserted replaced
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 -g 4 -@ 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