Mercurial > repos > nml > mykrobe_parser

annotate test-data/prediction_2020/data/SRR3500411_MMUN.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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6
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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1 {
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2 "SRR3500411_MMUN": {
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3 "susceptibility": {
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4 "Ofloxacin": {
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5 "predict": "S"
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6 },
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7 "Moxifloxacin": {
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8 "predict": "S"
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9 },
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10 "Isoniazid": {
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11 "predict": "S"
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12 },
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13 "Kanamycin": {
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14 "predict": "S"
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15 },
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16 "Ethambutol": {
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17 "predict": "S"
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18 },
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20 "predict": "S"
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21 },
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22 "Ciprofloxacin": {
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23 "predict": "S"
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24 },
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25 "Pyrazinamide": {
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26 "predict": "S"
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27 },
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28 "Rifampicin": {
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29 "predict": "S"
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30 },
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31 "Amikacin": {
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32 "predict": "S"
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33 },
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34 "Capreomycin": {
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35 "predict": "S"
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36 }
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37 },
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38 "phylogenetics": {
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39 "phylo_group": {
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40 "Mycobacterium_tuberculosis_complex": {
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41 "percent_coverage": 99.568,
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42 "median_depth": 114.0
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43 }
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46 "Unknown": {
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49 }
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50 },
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52 "Mycobacterium_africanum": {
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55 }
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56 },
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59 "clade_animal_A1"
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61 "calls_summary": {
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62 "clade_animal_A1": {
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65 "genotypes": {
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66 "clade_animal_A1": 1
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67 }
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69 },
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70 "calls": {
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72 "clade_animal_A1": {
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73 "G2873278T": {
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74 "variant": "ref-G2873278T?var_name=G2873278T&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G2873278T",
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75 "genotype": [
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76 1,
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78 ],
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79 "genotype_likelihoods": [
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84 "info": {
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98 "klen": 21
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99 }
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101 "expected_depths": [
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103 ],
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104 "contamination_depths": [],
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105 "filter": [],
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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106 "conf": 10811
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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107 },
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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108 "_cls": "Call.VariantCall"
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109 }
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110 }
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111 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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112 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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113 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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114 },
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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115 "kmer": 21,
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116 "probe_sets": [
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117 "tb-species-170421.fasta.gz",
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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118 "tb-hunt-probe-set-jan-03-2019.fasta.gz",
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119 "tb.lineage.20200930.probes.fa.gz"
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120 ],
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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121 "files": [
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122 "SRR3500411_1.fastq",
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123 "SRR3500411_2.fastq"
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124 ],
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125 "version": {
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126 "mykrobe-predictor": "v0.10.0",
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127 "mykrobe-atlas": "v0.10.0"
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128 },
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129 "genotype_model": "kmer_count"
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130 }
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131 }