Mercurial > repos > iuc > hamronize_tool

annotate test-data/mykrobe/mykrobe.json @ 4:cbfa52c8f1ef draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
author iuc
date Tue, 05 Mar 2024 19:47:12 +0000
parents
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Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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4
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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1 {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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2 "SRR6916544": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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3 "susceptibility": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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4 "Rifampicin": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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5 "predict": "r",
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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6 "called_by": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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7 "rpoB_S450L-TCG761154TTG": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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8 "variant": null,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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9 "genotype": [
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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10 0,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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11 1
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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12 ],
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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13 "genotype_likelihoods": [
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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14 -3594.140082249598,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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15 -136.57739012799902,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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16 -2127.6812715680494
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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17 ],
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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18 "info": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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19 "coverage": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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20 "reference": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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21 "percent_coverage": 100.0,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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22 "median_depth": 40,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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23 "min_non_zero_depth": 32,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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24 "kmer_count": 796,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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25 "klen": 21
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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26 },
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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27 "alternate": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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28 "percent_coverage": 100.0,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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29 "median_depth": 60,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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30 "min_non_zero_depth": 58,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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31 "kmer_count": 1150,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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32 "klen": 20
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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33 }
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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34 },
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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35 "expected_depths": [
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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36 124
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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37 ],
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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38 "contamination_depths": [],
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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39 "filter": [],
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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40 "conf": 3458
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iuc
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41 },
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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42 "_cls": "Call.VariantCall"
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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43 }
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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44 }
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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45 }
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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diff changeset
46 },
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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47 "phylogenetics": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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48 "phylo_group": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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49 "Mycobacterium_tuberculosis_complex": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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50 "percent_coverage": 99.681,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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51 "median_depth": 124
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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52 }
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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53 },
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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54 "sub_complex": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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55 "Unknown": {
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56 "percent_coverage": -1,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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diff changeset
57 "median_depth": -1
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents:
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58 }
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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diff changeset
59 },
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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60 "species": {
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iuc
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61 "Mycobacterium_tuberculosis": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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62 "percent_coverage": 98.804,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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63 "median_depth": 121
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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64 }
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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65 },
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66 "lineage": {
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67 "lineage": [
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68 "lineage2.2.10",
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69 "lineage3"
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70 ],
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iuc
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71 "calls_summary": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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72 "lineage2.2.10": {
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73 "good_nodes": 3,
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74 "tree_depth": 3,
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75 "genotypes": {
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76 "lineage2": 0.5,
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77 "lineage2.2": 0.5,
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diff changeset
78 "lineage2.2.10": 0.5
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iuc
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79 }
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents:
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80 },
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81 "lineage3": {
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82 "good_nodes": 1,
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iuc
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83 "tree_depth": 1,
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iuc
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diff changeset
84 "genotypes": {
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diff changeset
85 "lineage3": 0.5
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iuc
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86 }
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
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87 }
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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88 },
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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89 "calls": {
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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90 "lineage2.2.10": {
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91 "lineage2": {
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92 "G497491A": {
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93 "variant": "ref-G497491A?var_name=G497491A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=G497491A",
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents:
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94 "genotype": [
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
iuc
parents:
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95 0,
cbfa52c8f1ef planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hamronization commit b49fc153425676a82e77dec090676403112bcbe6
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96 1
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194 "kmer_count": 848,
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198 "expected_depths": [
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199 124
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201 "contamination_depths": [],
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202 "filter": [],
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203 "conf": 2215
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204 },
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205 "_cls": "Call.VariantCall"
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208 },
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209 "lineage3": {
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210 "lineage3": {
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211 "C3273107A": {
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212 "variant": "ref-C3273107A?var_name=C3273107A&num_alts=1&ref=NC_000962.3&enum=0&gene=NA&mut=C3273107A",
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213 "genotype": [
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214 0,
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215 1
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217 "genotype_likelihoods": [
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218 -3093.863597972382,
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222 "info": {
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223 "coverage": {
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224 "reference": {
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225 "percent_coverage": 100.0,
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226 "median_depth": 66,
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227 "min_non_zero_depth": 64,
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228 "kmer_count": 1323,
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229 "klen": 21
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230 },
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231 "alternate": {
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232 "percent_coverage": 100.0,
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233 "median_depth": 58,
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234 "min_non_zero_depth": 54,
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235 "kmer_count": 1160,
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236 "klen": 21
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237 }
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238 },
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239 "expected_depths": [
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240 124
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241 ],
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242 "contamination_depths": [],
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243 "filter": [],
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244 "conf": 3074
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245 },
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246 "_cls": "Call.VariantCall"
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247 }
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248 }
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249 }
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250 }
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251 }
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252 },
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253 "kmer": 21,
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254 "probe_sets": [
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255 "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb-species-170421.fasta.gz",
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256 "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb-hunt-probe-set-jan-03-2019.fasta.gz",
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257 "/home/pvh/miniconda3/envs/mykrobe/lib/python3.9/site-packages/mykrobe/data/tb/tb.lineage.20200930.probes.fa.gz"
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258 ],
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259 "files": [
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260 "../SRR6916544_1.fastq.gz",
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261 "../SRR6916544_2.fastq.gz"
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263 "version": {
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264 "mykrobe-predictor": "v0.10.0",
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265 "mykrobe-atlas": "v0.10.0"
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266 },
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267 "genotype_model": "kmer_count"
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268 }
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269 }