Mercurial > repos > nml > mykrobe_parser

annotate test-data/prediction_2020/data/ERR125628_MBOV.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
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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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 "ERR125628_MBOV": {
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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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19 "Streptomycin": {
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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": "R",
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27 "called_by": {
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28 "pncA_H57D-GTG2289071GTC": {
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29 "variant": null,
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30 "genotype": [
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31 1,
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32 1
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34 "genotype_likelihoods": [
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35 -5562.061052007205,
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36 -99999999,
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38 ],
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39 "info": {
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40 "coverage": {
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41 "reference": {
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42 "percent_coverage": 5.0,
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43 "median_depth": 0,
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44 "min_non_zero_depth": 44,
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45 "kmer_count": 44,
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46 "klen": 21
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47 },
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48 "alternate": {
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49 "percent_coverage": 100.0,
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50 "median_depth": 46,
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51 "min_non_zero_depth": 44,
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52 "kmer_count": 837,
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53 "klen": 19
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54 }
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55 },
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56 "expected_depths": [
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57 56.0
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58 ],
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59 "contamination_depths": [],
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60 "filter": [],
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61 "conf": 5473
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62 },
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63 "_cls": "Call.VariantCall"
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64 }
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65 }
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66 },
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67 "Rifampicin": {
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68 "predict": "S"
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69 },
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70 "Amikacin": {
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71 "predict": "S"
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72 },
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73 "Capreomycin": {
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74 "predict": "S"
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75 }
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76 },
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77 "phylogenetics": {
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78 "phylo_group": {
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79 "Mycobacterium_tuberculosis_complex": {
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80 "percent_coverage": 99.425,
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81 "median_depth": 56.0
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82 }
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83 },
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84 "sub_complex": {
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85 "Unknown": {
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86 "percent_coverage": -1,
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87 "median_depth": -1
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88 }
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89 },
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90 "species": {
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91 "Mycobacterium_bovis": {
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92 "percent_coverage": 65.402,
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93 "median_depth": 48.0
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94 }
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95 },
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96 "lineage": {
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97 "lineage": [
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98 "lineageBovis"
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99 ],
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100 "calls_summary": {
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101 "lineageBovis": {
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102 "good_nodes": 1,
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103 "tree_depth": 1,
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104 "genotypes": {
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105 "lineageBovis": 1
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106 }
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107 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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108 },
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109 "calls": {
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110 "lineageBovis": {
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111 "lineageBovis": {
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112 "C1492605T": {
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113 "variant": "ref-C1492605T?var_name=C1492605T&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=C1492605T",
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114 "genotype": [
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115 1,
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116 1
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117 ],
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118 "genotype_likelihoods": [
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119 -7771.156050282547,
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120 -99999999,
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121 -102.4977035173431
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122 ],
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123 "info": {
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124 "coverage": {
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125 "reference": {
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126 "percent_coverage": 60.0,
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127 "median_depth": 1,
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128 "min_non_zero_depth": 1,
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129 "kmer_count": 12,
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130 "klen": 21
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131 },
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132 "alternate": {
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133 "percent_coverage": 100.0,
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134 "median_depth": 82,
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135 "min_non_zero_depth": 75,
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136 "kmer_count": 1670,
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137 "klen": 21
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138 }
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139 },
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140 "expected_depths": [
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141 56.0
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142 ],
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143 "contamination_depths": [],
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144 "filter": [],
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145 "conf": 7669
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146 },
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147 "_cls": "Call.VariantCall"
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148 }
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149 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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150 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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151 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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152 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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153 },
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154 "kmer": 21,
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155 "probe_sets": [
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diff changeset
156 "tb-species-170421.fasta.gz",
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diff changeset
157 "tb-hunt-probe-set-jan-03-2019.fasta.gz",
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158 "tb.lineage.20200930.probes.fa.gz"
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159 ],
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diff changeset
160 "files": [
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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diff changeset
161 "ERR125628_1.fastq",
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diff changeset
162 "ERR125628_2.fastq"
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163 ],
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164 "version": {
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165 "mykrobe-predictor": "v0.10.0",
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166 "mykrobe-atlas": "v0.10.0"
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167 },
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168 "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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169 }
8e7e5a660942 planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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170 }