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comparison test-data/11.stats.expected @ 4:8d500e0e0dbe draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tool_collections/samtools/samtools_stats commit 70b38ebad0d0936f102e3e7cb70f1060347ea8c4
author iuc
date Thu, 27 Sep 2018 08:59:54 -0400
parents
children ab75c7ea49a5
comparison
equal deleted inserted replaced
3:45c568e7f1f9 4:8d500e0e0dbe
1 # CHK, Checksum [2]Read Names [3]Sequences [4]Qualities
2 # CHK, CRC32 of reads which passed filtering followed by addition (32bit overflow)
3 CHK cb2d2d82 bcd83869 62ec814e
4 # Summary Numbers. Use `grep ^SN | cut -f 2-` to extract this part.
5 SN raw total sequences: 26
6 SN filtered sequences: 0
7 SN sequences: 26
8 SN is sorted: 1
9 SN 1st fragments: 14
10 SN last fragments: 12
11 SN reads mapped: 26
12 SN reads mapped and paired: 26 # paired-end technology bit set + both mates mapped
13 SN reads unmapped: 0
14 SN reads properly paired: 24 # proper-pair bit set
15 SN reads paired: 26 # paired-end technology bit set
16 SN reads duplicated: 0 # PCR or optical duplicate bit set
17 SN reads MQ0: 1 # mapped and MQ=0
18 SN reads QC failed: 0
19 SN non-primary alignments: 0
20 SN total length: 260 # ignores clipping
21 SN total first fragment length: 140 # ignores clipping
22 SN total last fragment length: 120 # ignores clipping
23 SN bases mapped: 260 # ignores clipping
24 SN bases mapped (cigar): 206 # more accurate
25 SN bases trimmed: 0
26 SN bases duplicated: 0
27 SN mismatches: 0 # from NM fields
28 SN error rate: 0.000000e+00 # mismatches / bases mapped (cigar)
29 SN average length: 10
30 SN average first fragment length: 10
31 SN average last fragment length: 10
32 SN maximum length: 10
33 SN maximum first fragment length: 10
34 SN maximum last fragment length: 10
35 SN average quality: 13.1
36 SN insert size average: 34.0
37 SN insert size standard deviation: 0.0
38 SN inward oriented pairs: 12
39 SN outward oriented pairs: 0
40 SN pairs with other orientation: 0
41 SN pairs on different chromosomes: 1
42 SN percentage of properly paired reads (%): 92.3
43 SN bases inside the target: 42
44 SN percentage of target genome with coverage > 0 (%): 100.00
45 # First Fragment Qualities. Use `grep ^FFQ | cut -f 2-` to extract this part.
46 # Columns correspond to qualities and rows to cycles. First column is the cycle number.
47 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
48 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
49 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
50 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
51 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
52 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
53 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
54 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
55 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
56 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
57 # Last Fragment Qualities. Use `grep ^LFQ | cut -f 2-` to extract this part.
58 # Columns correspond to qualities and rows to cycles. First column is the cycle number.
59 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
60 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
61 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
62 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
63 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
64 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
65 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
66 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
67 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
68 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
69 # GC Content of first fragments. Use `grep ^GCF | cut -f 2-` to extract this part.
70 GCF 19.85 0
71 GCF 44.72 1
72 GCF 54.77 4
73 GCF 64.82 2
74 GCF 74.87 4
75 GCF 84.92 3
76 # GC Content of last fragments. Use `grep ^GCL | cut -f 2-` to extract this part.
77 GCL 19.85 0
78 GCL 44.72 2
79 GCL 59.80 3
80 GCL 74.87 4
81 # 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 [%]
82 GCC 1 19.23 42.31 15.38 23.08 0.00 0.00
83 GCC 2 19.23 19.23 46.15 15.38 0.00 0.00
84 GCC 3 23.08 38.46 19.23 19.23 0.00 0.00
85 GCC 4 23.08 23.08 38.46 15.38 0.00 0.00
86 GCC 5 11.54 38.46 26.92 23.08 0.00 0.00
87 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
89 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
91 GCC 10 23.08 23.08 38.46 15.38 0.00 0.00
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 [%]
93 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
95 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
97 FBC 5 14.29 35.71 35.71 14.29 0.00 0.00
98 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
100 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
102 FBC 10 14.29 28.57 35.71 21.43 0.00 0.00
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 [%]
104 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
106 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
108 LBC 5 8.33 41.67 16.67 33.33 0.00 0.00
109 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
111 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
113 LBC 10 33.33 16.67 41.67 8.33 0.00 0.00
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
115 IS 0 0 0 0 0
116 IS 1 0 0 0 0
117 IS 2 0 0 0 0
118 IS 3 0 0 0 0
119 IS 4 0 0 0 0
120 IS 5 0 0 0 0
121 IS 6 0 0 0 0
122 IS 7 0 0 0 0
123 IS 8 0 0 0 0
124 IS 9 0 0 0 0
125 IS 10 0 0 0 0
126 IS 11 0 0 0 0
127 IS 12 0 0 0 0
128 IS 13 0 0 0 0
129 IS 14 0 0 0 0
130 IS 15 0 0 0 0
131 IS 16 0 0 0 0
132 IS 17 0 0 0 0
133 IS 18 0 0 0 0
134 IS 19 0 0 0 0
135 IS 20 0 0 0 0
136 IS 21 0 0 0 0
137 IS 22 0 0 0 0
138 IS 23 0 0 0 0
139 IS 24 0 0 0 0
140 IS 25 0 0 0 0
141 IS 26 0 0 0 0
142 IS 27 0 0 0 0
143 IS 28 0 0 0 0
144 IS 29 0 0 0 0
145 IS 30 0 0 0 0
146 IS 31 0 0 0 0
147 IS 32 0 0 0 0
148 IS 33 0 0 0 0
149 IS 34 12 12 0 0
150 # Read lengths. Use `grep ^RL | cut -f 2-` to extract this part. The columns are: read length, count
151 RL 10 26
152 # Read lengths - first fragments. Use `grep ^FRL | cut -f 2-` to extract this part. The columns are: read length, count
153 FRL 10 14
154 # Read lengths - last fragments. Use `grep ^LRL | cut -f 2-` to extract this part. The columns are: read length, count
155 LRL 10 12
156 # Indel distribution. Use `grep ^ID | cut -f 2-` to extract this part. The columns are: length, number of insertions, number of deletions
157 # 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)
158 # Coverage distribution. Use `grep ^COV | cut -f 2-` to extract this part.
159 COV [1-1] 1 1
160 COV [2-2] 2 1
161 COV [3-3] 3 2
162 COV [4-4] 4 2
163 COV [5-5] 5 23
164 COV [6-6] 6 13
165 # 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
166 GCD 0.0 100.000 0.000 0.000 0.000 0.000 0.000