Mercurial > repos > nml > mykrobe_parser

annotate test-data/prediction_2020/data/ERR234162_L3.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 "ERR234162_L3": {
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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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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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20 "predict": "S"
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21 },
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23 "predict": "S"
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24 },
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26 "predict": "S"
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27 },
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29 "predict": "S"
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32 "predict": "S"
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35 "predict": "S"
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36 }
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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": 99.797,
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42 "median_depth": 157.0
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95 "alternate": {
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101 }
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103 "expected_depths": [
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104 157.0
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105 ],
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106 "contamination_depths": [],
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107 "filter": [],
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108 "conf": 22276
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109 },
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110 "_cls": "Call.VariantCall"
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111 }
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112 },
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113 "lineage3.1": null,
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114 "lineage3.1.1": {
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115 "G1084911A": {
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116 "variant": "ref-G1084911A?var_name=G1084911A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G1084911A",
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117 "genotype": [
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118 1,
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119 1
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120 ],
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121 "genotype_likelihoods": [
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122 -18914.2001312626,
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123 -99999999,
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124 -142.3141204554317
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125 ],
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126 "info": {
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127 "coverage": {
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128 "reference": {
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129 "percent_coverage": 0.0,
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130 "median_depth": 0,
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131 "min_non_zero_depth": 0,
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132 "kmer_count": 0,
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133 "klen": 21
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134 },
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135 "alternate": {
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136 "percent_coverage": 100.0,
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137 "median_depth": 149,
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138 "min_non_zero_depth": 145,
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139 "kmer_count": 3039,
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140 "klen": 21
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141 }
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142 },
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143 "expected_depths": [
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144 157.0
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145 ],
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146 "contamination_depths": [],
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147 "filter": [],
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148 "conf": 18772
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149 },
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150 "_cls": "Call.VariantCall"
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151 }
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152 }
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153 }
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154 }
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155 }
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156 },
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157 "kmer": 21,
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158 "probe_sets": [
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159 "tb-species-170421.fasta.gz",
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160 "tb-hunt-probe-set-jan-03-2019.fasta.gz",
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161 "tb.lineage.20200930.probes.fa.gz"
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162 ],
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163 "files": [
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164 "ERR234162_1.fastq",
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165 "ERR234162_2.fastq"
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166 ],
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167 "version": {
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168 "mykrobe-predictor": "v0.10.0",
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169 "mykrobe-atlas": "v0.10.0"
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170 },
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171 "genotype_model": "kmer_count"
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172 }
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173 }