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planemo upload for repository https://github.com/public-health-bioinformatics/galaxy_tools/blob/master/tools/tbprofiler_json_to_tabular commit 24535690aedb81353cf5e036dc4577022d9604ad
author public-health-bioinformatics
date Tue, 19 Sep 2023 18:03:41 +0000
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-1:000000000000 0:3e0d5ceeeb0f
1 {
2 "qc": {
3 "pct_reads_mapped": 99.47,
4 "num_reads_mapped": 1731409,
5 "median_coverage": 84,
6 "gene_coverage": [
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258 }
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261 },
262 "delly": "success",
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268 "rd": "None",
269 "frac": 1.0
270 },
271 {
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275 "rd": "RD122",
276 "frac": 1.0
277 }
278 ],
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292 "annotation": [
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297 }
298 ],
299 "alternate_consequences": [],
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309 }
310 ]
311 },
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319 "type": "upstream_gene_variant",
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321 "protein_change": "",
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333 },
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339 }
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362 "moxifloxacin",
363 "fluoroquinolones"
364 ]
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375 "protein_change": "p.Ser95Thr",
376 "annotation": [
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379 "lineage": "lineage4"
380 }
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388 "ciprofloxacin",
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392 ]
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394 {
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407 "gene": "gyrA",
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410 "ciprofloxacin",
411 "ofloxacin",
412 "moxifloxacin",
413 "fluoroquinolones"
414 ]
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416 {
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423 "type": "missense_variant",
424 "nucleotide_change": "c.2003G>A",
425 "protein_change": "p.Gly668Asp",
426 "alternate_consequences": [],
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428 "locus_tag": "Rv0006",
429 "gene": "gyrA",
430 "gene_associated_drugs": [
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432 "ciprofloxacin",
433 "ofloxacin",
434 "moxifloxacin",
435 "fluoroquinolones"
436 ]
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438 {
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445 "type": "synonymous_variant",
446 "nucleotide_change": "c.3420G>A",
447 "protein_change": "p.Glu1140Glu",
448 "alternate_consequences": [],
449 "change": "c.3420G>A",
450 "locus_tag": "Rv0668",
451 "gene": "rpoC",
452 "gene_associated_drugs": [
453 "rifampicin"
454 ]
455 },
456 {
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458 "genome_pos": 781395,
459 "ref": "T",
460 "alt": "C",
461 "freq": 1.0,
462 "feature_id": "CCP43425",
463 "type": "upstream_gene_variant",
464 "nucleotide_change": "c.-165T>C",
465 "protein_change": "",
466 "alternate_consequences": [],
467 "change": "c.-165T>C",
468 "locus_tag": "Rv0682",
469 "gene": "rpsL",
470 "gene_associated_drugs": [
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472 ]
473 },
474 {
475 "chrom": "Chromosome",
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477 "ref": "CGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT",
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480 "feature_id": "CCP43929",
481 "type": "frameshift_variant&stop_lost&splice_region_variant",
482 "nucleotide_change": "c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT",
483 "protein_change": "p.Ala855fs",
484 "alternate_consequences": [],
485 "change": "c.2565_*55delGGCCTAGCCCCGGCGACGATGCCGGGTCGCGGGATGCGGCCCGTTGAGGAGCGGGGCAATCT",
486 "locus_tag": "Rv1173",
487 "gene": "fbiC",
488 "gene_associated_drugs": [
489 "delamanid"
490 ]
491 },
492 {
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496 "alt": "T",
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498 "feature_id": "CCP44062",
499 "type": "upstream_gene_variant",
500 "nucleotide_change": "c.-69C>T",
501 "protein_change": "",
502 "alternate_consequences": [],
503 "change": "c.-69C>T",
504 "locus_tag": "Rv1305",
505 "gene": "atpE",
506 "gene_associated_drugs": [
507 "bedaquiline"
508 ]
509 },
510 {
511 "chrom": "Chromosome",
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513 "ref": "C",
514 "alt": "T",
515 "freq": 1.0,
516 "feature_id": "EBG00000313325-1",
517 "type": "upstream_gene_variant",
518 "nucleotide_change": "n.-187C>T",
519 "protein_change": "",
520 "alternate_consequences": [],
521 "change": "n.-187C>T",
522 "locus_tag": "EBG00000313325",
523 "gene": "rrs",
524 "gene_associated_drugs": [
525 "aminoglycosides",
526 "streptomycin",
527 "amikacin",
528 "capreomycin",
529 "kanamycin"
530 ]
531 },
532 {
533 "chrom": "Chromosome",
534 "genome_pos": 1917972,
535 "ref": "A",
536 "alt": "G",
537 "freq": 1.0,
538 "feature_id": "CCP44459",
539 "type": "synonymous_variant",
540 "nucleotide_change": "c.33A>G",
541 "protein_change": "p.Leu11Leu",
542 "alternate_consequences": [],
543 "change": "c.33A>G",
544 "locus_tag": "Rv1694",
545 "gene": "tlyA",
546 "gene_associated_drugs": [
547 "capreomycin"
548 ]
549 },
550 {
551 "chrom": "Chromosome",
552 "genome_pos": 3073868,
553 "ref": "T",
554 "alt": "C",
555 "freq": 1.0,
556 "feature_id": "CCP45563",
557 "type": "missense_variant",
558 "nucleotide_change": "c.604A>G",
559 "protein_change": "p.Thr202Ala",
560 "alternate_consequences": [],
561 "change": "p.Thr202Ala",
562 "locus_tag": "Rv2764c",
563 "gene": "thyA",
564 "gene_associated_drugs": [
565 "para-aminosalicylic_acid"
566 ]
567 },
568 {
569 "chrom": "Chromosome",
570 "genome_pos": 4242643,
571 "ref": "C",
572 "alt": "T",
573 "freq": 1.0,
574 "feature_id": "CCP46623",
575 "type": "upstream_gene_variant",
576 "nucleotide_change": "c.-590C>T",
577 "protein_change": "",
578 "alternate_consequences": [
579 {
580 "gene_name": "embC",
581 "gene_id": "Rv3793",
582 "feature_id": "CCP46622",
583 "type": "synonymous_variant",
584 "nucleotide_change": "c.2781C>T",
585 "protein_change": "p.Arg927Arg"
586 }
587 ],
588 "change": "c.-590C>T",
589 "locus_tag": "Rv3794",
590 "gene": "embA",
591 "gene_associated_drugs": [
592 "ethambutol"
593 ]
594 },
595 {
596 "chrom": "Chromosome",
597 "genome_pos": 1305494,
598 "ref": "C",
599 "alt": "<DEL>",
600 "freq": 1.0,
601 "feature_id": "CCP43929",
602 "type": "frameshift_variant&stop_lost&splice_region_variant",
603 "nucleotide_change": "c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN",
604 "protein_change": "p.Ala855fs",
605 "alternate_consequences": [],
606 "change": "c.2565_*56delCNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN",
607 "locus_tag": "Rv1173",
608 "gene": "fbiC",
609 "gene_associated_drugs": [
610 "delamanid"
611 ]
612 }
613 ],
614 "drtype": "MDR-TB",
615 "db_version": {
616 "name": "tbdb",
617 "commit": "7fc199d",
618 "Merge": "bad550a 277d053",
619 "Author": "Jody Phelan <jody.phelan@lshtm.ac.uk>",
620 "Date": "Tue Jan 25 17:21:48 2022 +0000"
621 },
622 "id": "tbprofiler",
623 "tbprofiler_version": "4.1.1",
624 "pipeline": [
625 {
626 "Analysis": "Mapping",
627 "Program": "bwa"
628 },
629 {
630 "Analysis": "Variant calling",
631 "Program": "freebayes"
632 }
633 ],
634 "timestamp": "22-10-2022 01:09:50"
635 }