Mercurial > repos > devteam > samtools_stats

comparison test-data/2.stats.expected @ 9:ab75c7ea49a5 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"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 16:08:22 +0000
parents 8d500e0e0dbe
children 8fecc86e574a
comparison
equal deleted inserted replaced
8:df598009c821 9:ab75c7ea49a5
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 --ref-seq reference.fa -@ 0 infile
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 1a1c1362 29c426ae 7bab45da 6 CHK 1a1c1362 29c426ae 7bab45da
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: 2 8 SN raw total sequences: 2 # excluding supplementary and secondary reads
6 SN filtered sequences: 0 9 SN filtered sequences: 0
7 SN sequences: 2 10 SN sequences: 2
8 SN is sorted: 1 11 SN is sorted: 1
9 SN 1st fragments: 1 12 SN 1st fragments: 1
10 SN last fragments: 1 13 SN last fragments: 1
15 SN reads paired: 2 # paired-end technology bit set 18 SN reads paired: 2 # 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: 0 # mapped and MQ=0 20 SN reads MQ0: 0 # 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: 70 # ignores clipping 24 SN total length: 70 # ignores clipping
21 SN total first fragment length: 35 # ignores clipping 25 SN total first fragment length: 35 # ignores clipping
22 SN total last fragment length: 35 # ignores clipping 26 SN total last fragment length: 35 # ignores clipping
23 SN bases mapped: 70 # ignores clipping 27 SN bases mapped: 70 # ignores clipping
24 SN bases mapped (cigar): 70 # more accurate 28 SN bases mapped (cigar): 70 # more accurate
193 GCC 31 0.00 100.00 0.00 0.00 0.00 0.00 197 GCC 31 0.00 100.00 0.00 0.00 0.00 0.00
194 GCC 32 0.00 50.00 50.00 0.00 0.00 0.00 198 GCC 32 0.00 50.00 50.00 0.00 0.00 0.00
195 GCC 33 50.00 0.00 0.00 50.00 0.00 0.00 199 GCC 33 50.00 0.00 0.00 50.00 0.00 0.00
196 GCC 34 50.00 0.00 50.00 0.00 0.00 0.00 200 GCC 34 50.00 0.00 50.00 0.00 0.00 0.00
197 GCC 35 0.00 0.00 50.00 50.00 0.00 0.00 201 GCC 35 0.00 0.00 50.00 50.00 0.00 0.00
202 # 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 [%]
203 GCT 1 0.00 50.00 0.00 50.00
204 GCT 2 50.00 0.00 50.00 0.00
205 GCT 3 0.00 0.00 50.00 50.00
206 GCT 4 0.00 0.00 100.00 0.00
207 GCT 5 0.00 0.00 50.00 50.00
208 GCT 6 0.00 50.00 0.00 50.00
209 GCT 7 0.00 0.00 50.00 50.00
210 GCT 8 0.00 0.00 0.00 100.00
211 GCT 9 0.00 50.00 50.00 0.00
212 GCT 10 50.00 0.00 50.00 0.00
213 GCT 11 50.00 0.00 0.00 50.00
214 GCT 12 50.00 0.00 50.00 0.00
215 GCT 13 50.00 0.00 50.00 0.00
216 GCT 14 0.00 0.00 0.00 100.00
217 GCT 15 100.00 0.00 0.00 0.00
218 GCT 16 50.00 0.00 0.00 50.00
219 GCT 17 0.00 0.00 50.00 50.00
220 GCT 18 0.00 50.00 50.00 0.00
221 GCT 19 0.00 100.00 0.00 0.00
222 GCT 20 0.00 0.00 50.00 50.00
223 GCT 21 0.00 0.00 100.00 0.00
224 GCT 22 0.00 50.00 0.00 50.00
225 GCT 23 50.00 0.00 0.00 50.00
226 GCT 24 50.00 0.00 50.00 0.00
227 GCT 25 50.00 0.00 50.00 0.00
228 GCT 26 0.00 0.00 100.00 0.00
229 GCT 27 50.00 0.00 0.00 50.00
230 GCT 28 0.00 0.00 50.00 50.00
231 GCT 29 0.00 50.00 0.00 50.00
232 GCT 30 0.00 50.00 0.00 50.00
233 GCT 31 0.00 50.00 50.00 0.00
234 GCT 32 0.00 0.00 100.00 0.00
235 GCT 33 100.00 0.00 0.00 0.00
236 GCT 34 0.00 0.00 50.00 50.00
237 GCT 35 50.00 0.00 50.00 0.00
198 # 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 [%] 238 # 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 [%]
199 FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 239 FBC 1 0.00 0.00 0.00 100.00 0.00 0.00
200 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 240 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00
201 FBC 3 0.00 0.00 100.00 0.00 0.00 0.00 241 FBC 3 0.00 0.00 100.00 0.00 0.00 0.00
202 FBC 4 0.00 0.00 100.00 0.00 0.00 0.00 242 FBC 4 0.00 0.00 100.00 0.00 0.00 0.00
229 FBC 31 0.00 100.00 0.00 0.00 0.00 0.00 269 FBC 31 0.00 100.00 0.00 0.00 0.00 0.00
230 FBC 32 0.00 0.00 100.00 0.00 0.00 0.00 270 FBC 32 0.00 0.00 100.00 0.00 0.00 0.00
231 FBC 33 100.00 0.00 0.00 0.00 0.00 0.00 271 FBC 33 100.00 0.00 0.00 0.00 0.00 0.00
232 FBC 34 0.00 0.00 100.00 0.00 0.00 0.00 272 FBC 34 0.00 0.00 100.00 0.00 0.00 0.00
233 FBC 35 0.00 0.00 100.00 0.00 0.00 0.00 273 FBC 35 0.00 0.00 100.00 0.00 0.00 0.00
274 # 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
275 FTC 6 5 15 9 0
234 # 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 [%] 276 # 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 [%]
235 LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 277 LBC 1 0.00 0.00 100.00 0.00 0.00 0.00
236 LBC 2 0.00 0.00 0.00 100.00 0.00 0.00 278 LBC 2 0.00 0.00 0.00 100.00 0.00 0.00
237 LBC 3 100.00 0.00 0.00 0.00 0.00 0.00 279 LBC 3 100.00 0.00 0.00 0.00 0.00 0.00
238 LBC 4 0.00 100.00 0.00 0.00 0.00 0.00 280 LBC 4 0.00 100.00 0.00 0.00 0.00 0.00
265 LBC 31 0.00 100.00 0.00 0.00 0.00 0.00 307 LBC 31 0.00 100.00 0.00 0.00 0.00 0.00
266 LBC 32 0.00 100.00 0.00 0.00 0.00 0.00 308 LBC 32 0.00 100.00 0.00 0.00 0.00 0.00
267 LBC 33 0.00 0.00 0.00 100.00 0.00 0.00 309 LBC 33 0.00 0.00 0.00 100.00 0.00 0.00
268 LBC 34 100.00 0.00 0.00 0.00 0.00 0.00 310 LBC 34 100.00 0.00 0.00 0.00 0.00 0.00
269 LBC 35 0.00 0.00 0.00 100.00 0.00 0.00 311 LBC 35 0.00 0.00 0.00 100.00 0.00 0.00
312 # 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
313 LTC 11 10 5 9 0
270 # 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 314 # 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
271 IS 0 0 0 0 0 315 IS 0 0 0 0 0
272 IS 1 0 0 0 0 316 IS 1 0 0 0 0
273 IS 2 0 0 0 0 317 IS 2 0 0 0 0
274 IS 3 0 0 0 0 318 IS 3 0 0 0 0