Mercurial > repos > nml > mykrobe_parser

annotate test-data/prediction_2020/data/ERR3335753_L1.json @ 6:8e7e5a660942 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
author nml
date Fri, 22 Sep 2023 17:24:02 +0000
parents
children
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179 "_cls": "Call.VariantCall"
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190 "phylogenetics": {
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191 "phylo_group": {
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192 "Mycobacterium_tuberculosis_complex": {
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312 -20293.11207308055,
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313 -3214.134387325289,
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314 -14.413062967015499
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315 ],
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316 "info": {
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317 "coverage": {
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318 "reference": {
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319 "percent_coverage": 100.0,
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320 "median_depth": 3,
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321 "min_non_zero_depth": 2,
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322 "kmer_count": 55,
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323 "klen": 21
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diff changeset
324 },
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325 "alternate": {
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326 "percent_coverage": 100.0,
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327 "median_depth": 247,
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328 "min_non_zero_depth": 241,
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329 "kmer_count": 5008,
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330 "klen": 21
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331 }
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diff changeset
332 },
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333 "expected_depths": [
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334 236.0
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335 ],
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336 "contamination_depths": [],
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337 "filter": [],
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338 "conf": 20279
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339 },
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340 "_cls": "Call.VariantCall"
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341 }
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diff changeset
342 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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343 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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344 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
345 }
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diff changeset
346 },
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diff changeset
347 "kmer": 21,
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348 "probe_sets": [
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diff changeset
349 "tb-species-170421.fasta.gz",
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350 "tb-hunt-probe-set-jan-03-2019.fasta.gz",
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351 "tb.lineage.20200930.probes.fa.gz"
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352 ],
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diff changeset
353 "files": [
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diff changeset
354 "ERR3335753_1.fastq",
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diff changeset
355 "ERR3335753_2.fastq"
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diff changeset
356 ],
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diff changeset
357 "version": {
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358 "mykrobe-predictor": "v0.10.0",
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diff changeset
359 "mykrobe-atlas": "v0.10.0"
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diff changeset
360 },
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diff changeset
361 "genotype_model": "kmer_count"
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents:
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362 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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363 }