Mercurial > repos > nml > mykrobe_parser
annotate test-data/prediction_2020/data/SRR17089001.json @ 7:12b397ad8687 draft default tip
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 97945a3ad655f1a0f99f577d0d423124460d900a
author | nml |
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date | Tue, 24 Oct 2023 21:28:06 +0000 |
parents | 8e7e5a660942 |
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rev | line source |
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6
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents:
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1 { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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2 "SRR17089001": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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3 "susceptibility": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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4 "Ofloxacin": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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5 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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6 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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7 "Moxifloxacin": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
diff
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8 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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9 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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10 "Isoniazid": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
diff
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11 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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12 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
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13 "Kanamycin": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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14 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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15 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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16 "Ethambutol": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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17 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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18 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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19 "Streptomycin": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
diff
changeset
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20 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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21 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
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22 "Ciprofloxacin": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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23 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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24 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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25 "Pyrazinamide": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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26 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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27 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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28 "Rifampicin": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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29 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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30 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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31 "Amikacin": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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32 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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33 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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34 "Capreomycin": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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35 "predict": "S" |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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36 } |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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37 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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38 "phylogenetics": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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39 "phylo_group": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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40 "Mycobacterium_tuberculosis_complex": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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41 "percent_coverage": 99.448, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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42 "median_depth": 240.0 |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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43 } |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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44 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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45 "sub_complex": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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46 "Unknown": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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47 "percent_coverage": -1, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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48 "median_depth": -1 |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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49 } |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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50 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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51 "species": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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52 "Mycobacterium_africanum": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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53 "percent_coverage": 54.809, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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54 "median_depth": 263 |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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55 } |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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56 }, |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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57 "lineage": { |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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58 "lineage": [ |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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59 "clade_animal_A3" |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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60 ], |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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61 "calls_summary": { |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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62 "clade_animal_A3": { |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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63 "good_nodes": 1, |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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64 "tree_depth": 1, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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65 "genotypes": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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66 "clade_animal_A3": 1 |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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67 } |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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68 } |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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69 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
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70 "calls": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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71 "clade_animal_A3": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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72 "clade_animal_A3": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
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73 "T154276G": { |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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74 "variant": "ref-T154276G?var_name=T154276G&num_alts=2&ref=NC_000962.3&enum=0&gene=NA&mut=T154276G", |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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75 "genotype": [ |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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76 1, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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77 1 |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents:
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78 ], |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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79 "genotype_likelihoods": [ |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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80 -28853.072634655364, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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81 -99999999, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents:
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82 -233.08196525549602 |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents:
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83 ], |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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84 "info": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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85 "coverage": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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86 "reference": { |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
parents:
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87 "percent_coverage": 0.0, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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parents:
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88 "median_depth": 0, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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89 "min_non_zero_depth": 0, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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90 "kmer_count": 0, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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91 "klen": 21 |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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92 }, |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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93 "alternate": { |
8e7e5a660942
planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
nml
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94 "percent_coverage": 100.0, |
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95 "median_depth": 231, |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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96 "min_non_zero_depth": 227, |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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97 "kmer_count": 4627, |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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98 "klen": 21 |
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planemo upload for repository https://github.com/phac-nml/mykrobe-parser commit 077a66175f3666924b42f216bbcb671ee0d026f2
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99 } |
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100 }, |
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101 "expected_depths": [ |
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102 240.0 |
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103 ], |
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104 "contamination_depths": [], |
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105 "filter": [], |
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106 "conf": 28620 |
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107 }, |
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108 "_cls": "Call.VariantCall" |
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109 } |
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110 } |
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111 } |
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112 } |
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113 } |
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114 }, |
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115 "kmer": 21, |
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116 "probe_sets": [ |
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117 "tb-species-170421.fasta.gz", |
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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 ], |
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121 "files": [ |
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122 "SRR17089001_1.fastq", |
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123 "SRR17089001_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 } |