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comparison test-data/12.3reads.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 541082d03bef
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/6/5/e/dataset_65ea4e4d-a70d-4001-911d-9d81ff2829a6.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 09f8b87f 140798ec 2b989f07 6 CHK 09f8b87f 140798ec 2b989f07
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: 3 8 SN raw total sequences: 3 # excluding supplementary and secondary reads
6 SN filtered sequences: 0 9 SN filtered sequences: 0
7 SN sequences: 3 10 SN sequences: 3
8 SN is sorted: 1 11 SN is sorted: 1
9 SN 1st fragments: 1 12 SN 1st fragments: 1
10 SN last fragments: 2 13 SN last fragments: 2
15 SN reads paired: 3 # paired-end technology bit set 18 SN reads paired: 3 # 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: 300 # ignores clipping 24 SN total length: 300 # 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: 200 # ignores clipping 26 SN total last fragment length: 200 # ignores clipping
23 SN bases mapped: 300 # ignores clipping 27 SN bases mapped: 300 # ignores clipping
24 SN bases mapped (cigar): 300 # more accurate 28 SN bases mapped (cigar): 300 # more accurate
353 GCC 96 0.00 66.67 0.00 33.33 0.00 0.00 357 GCC 96 0.00 66.67 0.00 33.33 0.00 0.00
354 GCC 97 33.33 33.33 0.00 33.33 0.00 0.00 358 GCC 97 33.33 33.33 0.00 33.33 0.00 0.00
355 GCC 98 0.00 66.67 0.00 33.33 0.00 0.00 359 GCC 98 0.00 66.67 0.00 33.33 0.00 0.00
356 GCC 99 0.00 100.00 0.00 0.00 0.00 0.00 360 GCC 99 0.00 100.00 0.00 0.00 0.00 0.00
357 GCC 100 0.00 0.00 0.00 100.00 0.00 0.00 361 GCC 100 0.00 0.00 0.00 100.00 0.00 0.00
362 # 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 [%]
363 GCT 1 33.33 0.00 0.00 66.67
364 GCT 2 0.00 33.33 33.33 33.33
365 GCT 3 0.00 33.33 33.33 33.33
366 GCT 4 33.33 66.67 0.00 0.00
367 GCT 5 0.00 66.67 33.33 0.00
368 GCT 6 33.33 0.00 0.00 66.67
369 GCT 7 33.33 0.00 0.00 66.67
370 GCT 8 0.00 33.33 33.33 33.33
371 GCT 9 0.00 66.67 33.33 0.00
372 GCT 10 33.33 33.33 0.00 33.33
373 GCT 11 33.33 33.33 0.00 33.33
374 GCT 12 0.00 33.33 33.33 33.33
375 GCT 13 0.00 0.00 33.33 66.67
376 GCT 14 0.00 66.67 33.33 0.00
377 GCT 15 33.33 66.67 0.00 0.00
378 GCT 16 33.33 0.00 0.00 66.67
379 GCT 17 33.33 0.00 0.00 66.67
380 GCT 18 0.00 33.33 33.33 33.33
381 GCT 19 0.00 33.33 33.33 33.33
382 GCT 20 0.00 66.67 33.33 0.00
383 GCT 21 33.33 66.67 0.00 0.00
384 GCT 22 33.33 0.00 0.00 66.67
385 GCT 23 0.00 0.00 33.33 66.67
386 GCT 24 0.00 33.33 33.33 33.33
387 GCT 25 33.33 66.67 0.00 0.00
388 GCT 26 33.33 33.33 0.00 33.33
389 GCT 27 0.00 33.33 33.33 33.33
390 GCT 28 0.00 33.33 33.33 33.33
391 GCT 29 0.00 0.00 33.33 66.67
392 GCT 30 33.33 66.67 0.00 0.00
393 GCT 31 33.33 66.67 0.00 0.00
394 GCT 32 33.33 0.00 0.00 66.67
395 GCT 33 0.00 0.00 33.33 66.67
396 GCT 34 0.00 33.33 33.33 33.33
397 GCT 35 33.33 33.33 0.00 33.33
398 GCT 36 0.00 66.67 33.33 0.00
399 GCT 37 33.33 66.67 0.00 0.00
400 GCT 38 33.33 0.00 0.00 66.67
401 GCT 39 0.00 0.00 33.33 66.67
402 GCT 40 0.00 33.33 33.33 33.33
403 GCT 41 33.33 66.67 0.00 0.00
404 GCT 42 33.33 33.33 0.00 33.33
405 GCT 43 0.00 33.33 33.33 33.33
406 GCT 44 0.00 33.33 33.33 33.33
407 GCT 45 0.00 33.33 33.33 33.33
408 GCT 46 33.33 66.67 0.00 0.00
409 GCT 47 33.33 33.33 0.00 33.33
410 GCT 48 33.33 0.00 0.00 66.67
411 GCT 49 0.00 0.00 33.33 66.67
412 GCT 50 0.00 66.67 33.33 0.00
413 GCT 51 33.33 66.67 0.00 0.00
414 GCT 52 0.00 66.67 33.33 0.00
415 GCT 53 33.33 0.00 0.00 66.67
416 GCT 54 33.33 0.00 0.00 66.67
417 GCT 55 0.00 33.33 33.33 33.33
418 GCT 56 0.00 66.67 33.33 0.00
419 GCT 57 33.33 33.33 0.00 33.33
420 GCT 58 33.33 33.33 0.00 33.33
421 GCT 59 0.00 33.33 33.33 33.33
422 GCT 60 0.00 0.00 33.33 66.67
423 GCT 61 0.00 66.67 33.33 0.00
424 GCT 62 33.33 66.67 0.00 0.00
425 GCT 63 33.33 0.00 0.00 66.67
426 GCT 64 33.33 0.00 0.00 66.67
427 GCT 65 0.00 33.33 33.33 33.33
428 GCT 66 0.00 33.33 33.33 33.33
429 GCT 67 33.33 66.67 0.00 0.00
430 GCT 68 0.00 66.67 33.33 0.00
431 GCT 69 33.33 0.00 0.00 66.67
432 GCT 70 33.33 0.00 0.00 66.67
433 GCT 71 0.00 33.33 33.33 33.33
434 GCT 72 0.00 66.67 33.33 0.00
435 GCT 73 33.33 33.33 0.00 33.33
436 GCT 74 33.33 33.33 0.00 33.33
437 GCT 75 0.00 33.33 33.33 33.33
438 GCT 76 0.00 0.00 33.33 66.67
439 GCT 77 0.00 66.67 33.33 0.00
440 GCT 78 33.33 66.67 0.00 0.00
441 GCT 79 33.33 0.00 0.00 66.67
442 GCT 80 33.33 0.00 0.00 66.67
443 GCT 81 0.00 33.33 33.33 33.33
444 GCT 82 0.00 66.67 33.33 0.00
445 GCT 83 0.00 66.67 33.33 0.00
446 GCT 84 33.33 33.33 0.00 33.33
447 GCT 85 33.33 0.00 0.00 66.67
448 GCT 86 0.00 0.00 33.33 66.67
449 GCT 87 0.00 66.67 33.33 0.00
450 GCT 88 33.33 66.67 0.00 0.00
451 GCT 89 33.33 33.33 0.00 33.33
452 GCT 90 0.00 0.00 33.33 66.67
453 GCT 91 0.00 33.33 33.33 33.33
454 GCT 92 0.00 66.67 33.33 0.00
455 GCT 93 33.33 66.67 0.00 0.00
456 GCT 94 33.33 33.33 0.00 33.33
457 GCT 95 33.33 0.00 0.00 66.67
458 GCT 96 0.00 33.33 33.33 33.33
459 GCT 97 33.33 0.00 33.33 33.33
460 GCT 98 33.33 66.67 0.00 0.00
461 GCT 99 0.00 66.67 33.33 0.00
462 GCT 100 33.33 0.00 0.00 66.67
358 # 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 [%] 463 # 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 [%]
359 FBC 1 0.00 0.00 0.00 100.00 0.00 0.00 464 FBC 1 0.00 0.00 0.00 100.00 0.00 0.00
360 FBC 2 0.00 100.00 0.00 0.00 0.00 0.00 465 FBC 2 0.00 100.00 0.00 0.00 0.00 0.00
361 FBC 3 0.00 100.00 0.00 0.00 0.00 0.00 466 FBC 3 0.00 100.00 0.00 0.00 0.00 0.00
362 FBC 4 0.00 0.00 0.00 100.00 0.00 0.00 467 FBC 4 0.00 0.00 0.00 100.00 0.00 0.00
454 FBC 96 0.00 100.00 0.00 0.00 0.00 0.00 559 FBC 96 0.00 100.00 0.00 0.00 0.00 0.00
455 FBC 97 0.00 100.00 0.00 0.00 0.00 0.00 560 FBC 97 0.00 100.00 0.00 0.00 0.00 0.00
456 FBC 98 0.00 0.00 0.00 100.00 0.00 0.00 561 FBC 98 0.00 0.00 0.00 100.00 0.00 0.00
457 FBC 99 0.00 100.00 0.00 0.00 0.00 0.00 562 FBC 99 0.00 100.00 0.00 0.00 0.00 0.00
458 FBC 100 0.00 0.00 0.00 100.00 0.00 0.00 563 FBC 100 0.00 0.00 0.00 100.00 0.00 0.00
564 # 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
565 FTC 0 51 0 49 0
459 # 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 [%] 566 # 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 [%]
460 LBC 1 0.00 0.00 0.00 100.00 0.00 0.00 567 LBC 1 0.00 0.00 0.00 100.00 0.00 0.00
461 LBC 2 0.00 50.00 0.00 50.00 0.00 0.00 568 LBC 2 0.00 50.00 0.00 50.00 0.00 0.00
462 LBC 3 0.00 50.00 0.00 50.00 0.00 0.00 569 LBC 3 0.00 50.00 0.00 50.00 0.00 0.00
463 LBC 4 0.00 100.00 0.00 0.00 0.00 0.00 570 LBC 4 0.00 100.00 0.00 0.00 0.00 0.00
555 LBC 96 0.00 50.00 0.00 50.00 0.00 0.00 662 LBC 96 0.00 50.00 0.00 50.00 0.00 0.00
556 LBC 97 50.00 0.00 0.00 50.00 0.00 0.00 663 LBC 97 50.00 0.00 0.00 50.00 0.00 0.00
557 LBC 98 0.00 100.00 0.00 0.00 0.00 0.00 664 LBC 98 0.00 100.00 0.00 0.00 0.00 0.00
558 LBC 99 0.00 100.00 0.00 0.00 0.00 0.00 665 LBC 99 0.00 100.00 0.00 0.00 0.00 0.00
559 LBC 100 0.00 0.00 0.00 100.00 0.00 0.00 666 LBC 100 0.00 0.00 0.00 100.00 0.00 0.00
667 # 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
668 LTC 1 102 0 97 0
669 # 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 [%]
670 BCC1 2 0.00 0.00 100.00 0.00 0.00
671 BCC1 3 0.00 0.00 0.00 100.00 0.00
672 BCC1 4 0.00 100.00 0.00 0.00 0.00
673 BCC1 5 0.00 0.00 0.00 100.00 0.00
674 BCC1 6 100.00 0.00 0.00 0.00 0.00
675 BCC1 7 0.00 0.00 0.00 100.00 0.00
676 BCC1 8 0.00 100.00 0.00 0.00 0.00
677 # Barcode Qualities. Use `grep ^QTQ | cut -f 2-` to extract this part.
678 # Columns correspond to qualities and rows to barcode cycles. First column is the cycle number.
679 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
680 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
681 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
682 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
683 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 0 0 1
684 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
685 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
686 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
560 # 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 687 # 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
561 IS 0 0 0 0 0 688 IS 0 0 0 0 0
562 IS 1 0 0 0 0 689 IS 1 0 0 0 0
563 IS 2 0 0 0 0 690 IS 2 0 0 0 0
564 IS 3 0 0 0 0 691 IS 3 0 0 0 0