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comparison test-data/12.2reads.overlap.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 -t /tmp/tmp0r5zs075/files/2/a/2/dataset_2a2a3ee9-3133-4880-a37c-50b6354c9000.dat -@ 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 5b31676a b0edee94 471895da 6 CHK 5b31676a b0edee94 471895da
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: 200 # ignores clipping 24 SN total length: 200 # ignores clipping
21 SN total first fragment length: 100 # ignores clipping 25 SN total first fragment length: 100 # ignores clipping
22 SN total last fragment length: 100 # ignores clipping 26 SN total last fragment length: 100 # ignores clipping
23 SN bases mapped: 200 # ignores clipping 27 SN bases mapped: 200 # ignores clipping
24 SN bases mapped (cigar): 199 # more accurate 28 SN bases mapped (cigar): 199 # more accurate
351 GCC 96 50.00 50.00 0.00 0.00 0.00 0.00 355 GCC 96 50.00 50.00 0.00 0.00 0.00 0.00
352 GCC 97 50.00 50.00 0.00 0.00 0.00 0.00 356 GCC 97 50.00 50.00 0.00 0.00 0.00 0.00
353 GCC 98 50.00 50.00 0.00 0.00 0.00 0.00 357 GCC 98 50.00 50.00 0.00 0.00 0.00 0.00
354 GCC 99 50.00 50.00 0.00 0.00 0.00 0.00 358 GCC 99 50.00 50.00 0.00 0.00 0.00 0.00
355 GCC 100 100.00 0.00 0.00 0.00 0.00 0.00 359 GCC 100 100.00 0.00 0.00 0.00 0.00 0.00
360 # 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 [%]
361 GCT 1 50.00 0.00 50.00 0.00
362 GCT 2 0.00 50.00 50.00 0.00
363 GCT 3 0.00 50.00 0.00 50.00
364 GCT 4 0.00 50.00 50.00 0.00
365 GCT 5 0.00 0.00 50.00 50.00
366 GCT 6 0.00 0.00 50.00 50.00
367 GCT 7 0.00 50.00 0.00 50.00
368 GCT 8 0.00 0.00 50.00 50.00
369 GCT 9 0.00 50.00 0.00 50.00
370 GCT 10 50.00 0.00 50.00 0.00
371 GCT 11 0.00 0.00 100.00 0.00
372 GCT 12 50.00 0.00 0.00 50.00
373 GCT 13 0.00 50.00 50.00 0.00
374 GCT 14 50.00 0.00 0.00 50.00
375 GCT 15 0.00 0.00 50.00 50.00
376 GCT 16 0.00 50.00 50.00 0.00
377 GCT 17 0.00 50.00 0.00 50.00
378 GCT 18 100.00 0.00 0.00 0.00
379 GCT 19 50.00 0.00 0.00 50.00
380 GCT 20 0.00 50.00 50.00 0.00
381 GCT 21 50.00 0.00 0.00 50.00
382 GCT 22 0.00 50.00 0.00 50.00
383 GCT 23 0.00 0.00 0.00 100.00
384 GCT 24 0.00 50.00 50.00 0.00
385 GCT 25 0.00 0.00 0.00 100.00
386 GCT 26 0.00 0.00 50.00 50.00
387 GCT 27 0.00 100.00 0.00 0.00
388 GCT 28 0.00 0.00 0.00 100.00
389 GCT 29 50.00 0.00 50.00 0.00
390 GCT 30 0.00 50.00 0.00 50.00
391 GCT 31 0.00 50.00 0.00 50.00
392 GCT 32 0.00 0.00 50.00 50.00
393 GCT 33 0.00 50.00 0.00 50.00
394 GCT 34 50.00 0.00 0.00 50.00
395 GCT 35 0.00 50.00 0.00 50.00
396 GCT 36 0.00 100.00 0.00 0.00
397 GCT 37 0.00 50.00 0.00 50.00
398 GCT 38 50.00 50.00 0.00 0.00
399 GCT 39 100.00 0.00 0.00 0.00
400 GCT 40 0.00 0.00 100.00 0.00
401 GCT 41 0.00 50.00 0.00 50.00
402 GCT 42 50.00 50.00 0.00 0.00
403 GCT 43 0.00 0.00 50.00 50.00
404 GCT 44 50.00 0.00 50.00 0.00
405 GCT 45 50.00 0.00 50.00 0.00
406 GCT 46 50.00 0.00 50.00 0.00
407 GCT 47 50.00 0.00 50.00 0.00
408 GCT 48 0.00 50.00 50.00 0.00
409 GCT 49 50.00 0.00 0.00 50.00
410 GCT 50 0.00 0.00 50.00 50.00
411 GCT 51 0.00 0.00 100.00 0.00
412 GCT 52 50.00 0.00 50.00 0.00
413 GCT 53 0.00 50.00 0.00 50.00
414 GCT 54 50.00 0.00 50.00 0.00
415 GCT 55 50.00 0.00 0.00 50.00
416 GCT 56 0.00 50.00 50.00 0.00
417 GCT 57 100.00 0.00 0.00 0.00
418 GCT 58 50.00 0.00 50.00 0.00
419 GCT 59 100.00 0.00 0.00 0.00
420 GCT 60 50.00 0.00 50.00 0.00
421 GCT 61 0.00 0.00 0.00 100.00
422 GCT 62 0.00 50.00 50.00 0.00
423 GCT 63 50.00 0.00 0.00 50.00
424 GCT 64 0.00 0.00 100.00 0.00
425 GCT 65 50.00 50.00 0.00 0.00
426 GCT 66 0.00 50.00 0.00 50.00
427 GCT 67 0.00 0.00 0.00 100.00
428 GCT 68 0.00 50.00 0.00 50.00
429 GCT 69 0.00 50.00 0.00 50.00
430 GCT 70 50.00 0.00 0.00 50.00
431 GCT 71 0.00 0.00 0.00 100.00
432 GCT 72 0.00 50.00 0.00 50.00
433 GCT 73 0.00 0.00 0.00 100.00
434 GCT 74 0.00 50.00 0.00 50.00
435 GCT 75 50.00 0.00 0.00 50.00
436 GCT 76 0.00 50.00 0.00 50.00
437 GCT 77 50.00 0.00 0.00 50.00
438 GCT 78 50.00 0.00 0.00 50.00
439 GCT 79 50.00 0.00 0.00 50.00
440 GCT 80 50.00 0.00 0.00 50.00
441 GCT 81 50.00 0.00 0.00 50.00
442 GCT 82 50.00 0.00 0.00 50.00
443 GCT 83 50.00 0.00 0.00 50.00
444 GCT 84 50.00 0.00 0.00 50.00
445 GCT 85 50.00 0.00 0.00 50.00
446 GCT 86 50.00 0.00 0.00 50.00
447 GCT 87 50.00 0.00 0.00 50.00
448 GCT 88 50.00 0.00 0.00 50.00
449 GCT 89 50.00 0.00 0.00 50.00
450 GCT 90 50.00 0.00 0.00 50.00
451 GCT 91 50.00 0.00 50.00 0.00
452 GCT 92 50.00 0.00 50.00 0.00
453 GCT 93 50.00 0.00 50.00 0.00
454 GCT 94 50.00 0.00 0.00 50.00
455 GCT 95 50.00 0.00 50.00 0.00
456 GCT 96 50.00 0.00 50.00 0.00
457 GCT 97 50.00 0.00 50.00 0.00
458 GCT 98 50.00 0.00 50.00 0.00
459 GCT 99 50.00 0.00 50.00 0.00
460 GCT 100 50.00 0.00 0.00 50.00
356 # 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 [%] 461 # 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 [%]
357 FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 462 FBC 1 0.00 0.00 0.00 100.00 0.00 0.00
358 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00 463 FBC 2 0.00 0.00 100.00 0.00 0.00 0.00
359 FBC 3 100.00 0.00 0.00 0.00 0.00 0.00 464 FBC 3 100.00 0.00 0.00 0.00 0.00 0.00
360 FBC 4 0.00 0.00 100.00 0.00 0.00 0.00 465 FBC 4 0.00 0.00 100.00 0.00 0.00 0.00
452 FBC 96 0.00 100.00 0.00 0.00 0.00 0.00 557 FBC 96 0.00 100.00 0.00 0.00 0.00 0.00
453 FBC 97 0.00 100.00 0.00 0.00 0.00 0.00 558 FBC 97 0.00 100.00 0.00 0.00 0.00 0.00
454 FBC 98 0.00 100.00 0.00 0.00 0.00 0.00 559 FBC 98 0.00 100.00 0.00 0.00 0.00 0.00
455 FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 560 FBC 99 0.00 100.00 0.00 0.00 0.00 0.00
456 FBC 100 100.00 0.00 0.00 0.00 0.00 0.00 561 FBC 100 100.00 0.00 0.00 0.00 0.00 0.00
562 # 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
563 FTC 50 21 14 15 0
457 # 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 [%] 564 # 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 [%]
458 LBC 1 0.00 0.00 100.00 0.00 0.00 0.00 565 LBC 1 0.00 0.00 100.00 0.00 0.00 0.00
459 LBC 2 0.00 0.00 100.00 0.00 0.00 0.00 566 LBC 2 0.00 0.00 100.00 0.00 0.00 0.00
460 LBC 3 0.00 100.00 0.00 0.00 0.00 0.00 567 LBC 3 0.00 100.00 0.00 0.00 0.00 0.00
461 LBC 4 0.00 0.00 100.00 0.00 0.00 0.00 568 LBC 4 0.00 0.00 100.00 0.00 0.00 0.00
553 LBC 96 100.00 0.00 0.00 0.00 0.00 0.00 660 LBC 96 100.00 0.00 0.00 0.00 0.00 0.00
554 LBC 97 100.00 0.00 0.00 0.00 0.00 0.00 661 LBC 97 100.00 0.00 0.00 0.00 0.00 0.00
555 LBC 98 100.00 0.00 0.00 0.00 0.00 0.00 662 LBC 98 100.00 0.00 0.00 0.00 0.00 0.00
556 LBC 99 100.00 0.00 0.00 0.00 0.00 0.00 663 LBC 99 100.00 0.00 0.00 0.00 0.00 0.00
557 LBC 100 100.00 0.00 0.00 0.00 0.00 0.00 664 LBC 100 100.00 0.00 0.00 0.00 0.00 0.00
665 # 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
666 LTC 41 20 23 16 0
667 # 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 [%]
668 BCC1 2 0.00 0.00 100.00 0.00 0.00
669 BCC1 3 0.00 0.00 0.00 100.00 0.00
670 BCC1 4 0.00 100.00 0.00 0.00 0.00
671 BCC1 5 0.00 0.00 0.00 100.00 0.00
672 BCC1 6 100.00 0.00 0.00 0.00 0.00
673 BCC1 7 0.00 0.00 0.00 100.00 0.00
674 BCC1 8 0.00 100.00 0.00 0.00 0.00
675 # Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part.
676 # Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.
677 QTQ1 1 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
678 QTQ1 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0
679 QTQ1 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0
680 QTQ1 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
681 QTQ1 5 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
682 QTQ1 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
683 QTQ1 7 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1
684 QTQ1 8 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0
558 # 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 685 # 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
559 IS 0 0 0 0 0 686 IS 0 0 0 0 0
560 IS 1 0 0 0 0 687 IS 1 0 0 0 0
561 IS 2 0 0 0 0 688 IS 2 0 0 0 0
562 IS 3 0 0 0 0 689 IS 3 0 0 0 0