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comparison test-data/rif_resistant.results.json @ 3:42818629ec4c draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/blob/master/tools/tbvcfreport commit f54e7cfd572498517dde7fe6afab47a20e3fcb17
author iuc
date Fri, 31 May 2024 20:06:49 +0000
parents 02d81b994ef5
children
comparison
equal deleted inserted replaced
2:4934c0ac6197 3:42818629ec4c
1 {"missing_pos": [["Chromosome", 763404], ["Chromosome", 763405], ["Chromosome", 763406], ["Chromosome", 763407], ["Chromosome", 763408], ["Chromosome", 763409], ["Chromosome", 763410], ["Chromosome", 763411], ["Chromosome", 763412], ["Chromosome", 763413], ["Chromosome", 763414], ["Chromosome", 763415], ["Chromosome", 763416], ["Chromosome", 763417], ["Chromosome", 763418], ["Chromosome", 763419], ["Chromosome", 763420], ["Chromosome", 1834082], ["Chromosome", 1834083], ["Chromosome", 1834084], ["Chromosome", 1834085], ["Chromosome", 1834086], ["Chromosome", 1834087], ["Chromosome", 1834088], ["Chromosome", 1834089], ["Chromosome", 1834090], ["Chromosome", 1834091], ["Chromosome", 1834092], ["Chromosome", 1834093], ["Chromosome", 1834094], ["Chromosome", 1834095], ["Chromosome", 1834251], ["Chromosome", 1834252], ["Chromosome", 1834253], ["Chromosome", 1834254], ["Chromosome", 1834255], ["Chromosome", 1834256], ["Chromosome", 1834257], ["Chromosome", 1834258], ["Chromosome", 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2 "id": "tbprofiler",
3 "timestamp": "2024-05-31T15:43:38.437239",
4 "pipeline": {
5 "software_version": "6.2.1",
6 "db_version": {
7 "name": "tbdb",
8 "commit": "82777ea",
9 "Author": "Jody Phelan <jody.phelan@lshtm.ac.uk>",
10 "Date": "Sun Mar 17 01:14:00 2024 +0000"
11 },
12 "software": [
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14 "process": "variant_calling",
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16 },
17 {
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20 }
21 ]
22 },
23 "notes": [],
24 "lineage": [
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54 },
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70 }
71 ]
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102 }
103 ]
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126 }
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150 "type": "missense_variant",
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152 "nucleotide_change": "c.1304A>T",
153 "protein_change": "p.Asp435Val",
154 "annotation": [
155 {
156 "type": "drug_resistance",
157 "drug": "rifampicin",
158 "original_mutation": "p.Asp435Val",
159 "confidence": "Assoc w R",
160 "source": "WHO catalogue v2",
161 "comment": ""
162 }
163 ],
164 "consequences": [
165 {
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171 "protein_change": "p.Asp435Val",
172 "annotation": [
173 {
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178 "source": "WHO catalogue v2",
179 "comment": ""
180 },
181 {
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183 "drug": "rifampicin",
184 "original_mutation": "RRDR non-silent",
185 "confidence": "Assoc w R - Interim",
186 "source": "WHO catalogue v2",
187 "comment": "Expert rule: Non-silent variants in RRDR of rpoB"
188 }
189 ]
190 }
191 ],
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198 "source": "WHO catalogue v2",
199 "comment": ""
200 }
201 ],
202 "locus_tag": "Rv0667",
203 "gene_associated_drugs": [
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205 ]
206 }
207 ],
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226 "nucleotide_change": "c.3225T>C",
227 "protein_change": "p.Ala1075Ala",
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234 "source": "WHO catalogue v2",
235 "comment": ""
236 }
237 ],
238 "consequences": [
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252 "source": "WHO catalogue v2",
253 "comment": ""
254 }
255 ]
256 },
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259 "gene_name": "rpoC",
260 "feature_id": "CCP43411",
261 "type": "upstream_gene_variant",
262 "nucleotide_change": "c.-339T>C",
263 "protein_change": "",
264 "annotation": []
265 }
266 ],
267 "locus_tag": "Rv0667",
268 "gene_associated_drugs": [
269 "rifampicin"
270 ]
271 },
272 {
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285 "gene_name": "rpsA",
286 "feature_id": "CCP44394",
287 "type": "synonymous_variant",
288 "change": "c.636A>C",
289 "nucleotide_change": "c.636A>C",
290 "protein_change": "p.Arg212Arg",
291 "annotation": [
292 {
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294 "drug": "pyrazinamide",
295 "original_mutation": "c.636A>C",
296 "confidence": "Not assoc w R - Interim",
297 "source": "WHO catalogue v2",
298 "comment": ""
299 }
300 ],
301 "consequences": [
302 {
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304 "gene_name": "rpsA",
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306 "type": "synonymous_variant",
307 "nucleotide_change": "c.636A>C",
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309 "annotation": [
310 {
311 "type": "who_confidence",
312 "drug": "pyrazinamide",
313 "original_mutation": "c.636A>C",
314 "confidence": "Not assoc w R - Interim",
315 "source": "WHO catalogue v2",
316 "comment": ""
317 }
318 ]
319 }
320 ],
321 "locus_tag": "Rv1630",
322 "gene_associated_drugs": [
323 "pyrazinamide"
324 ]
325 }
326 ],
327 "qc_fail_variants": [],
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519 {
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591 "percent_depth_pass": 0.0,
592 "median_depth": 0.0
593 },
594 {
595 "target": "Rv3236c",
596 "percent_depth_pass": 0.0,
597 "median_depth": 0.0
598 },
599 {
600 "target": "lpqB",
601 "percent_depth_pass": 0.0,
602 "median_depth": 0.0
603 },
604 {
605 "target": "mtrB",
606 "percent_depth_pass": 0.0,
607 "median_depth": 0.0
608 },
609 {
610 "target": "mtrA",
611 "percent_depth_pass": 0.0,
612 "median_depth": 0.0
613 },
614 {
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617 "median_depth": 0.0
618 },
619 {
620 "target": "fbiB",
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622 "median_depth": 0.0
623 },
624 {
625 "target": "alr",
626 "percent_depth_pass": 0.0,
627 "median_depth": 0.0
628 },
629 {
630 "target": "rpoA",
631 "percent_depth_pass": 0.0,
632 "median_depth": 0.0
633 },
634 {
635 "target": "ddn",
636 "percent_depth_pass": 0.0,
637 "median_depth": 0.0
638 },
639 {
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642 "median_depth": 0.0
643 },
644 {
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647 "median_depth": 0.0
648 },
649 {
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652 "median_depth": 0.0
653 },
654 {
655 "target": "embC",
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657 "median_depth": 0.0
658 },
659 {
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662 "median_depth": 0.0
663 },
664 {
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667 "median_depth": 0.0
668 },
669 {
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672 "median_depth": 0.0
673 },
674 {
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679 {
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684 {
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689 {
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694 {
695 "target": "gid",
696 "percent_depth_pass": 0.0,
697 "median_depth": 0.0
698 }
699 ],
700 "missing_positions": [
701 ]
702 },
703 "linked_samples": []
704 }