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0
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1 {
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2 "software_result": {
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3 "type": "software_result",
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4 "key": "string*",
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5 "software_name": "string*",
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6 "software_version": "string*",
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7 "software_branch": "string",
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8 "software_commit": "string",
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9 "software_log": "string",
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10 "run_id": "string",
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11 "run_date": "date",
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12 "databases": "dict database:class",
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13 "genes": "dict gene:class",
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14 "seq_variations": "dict seq_variation:class",
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15 "phenotypes": "dict phenotype:class"
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16 },
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17 "database": {
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18 "type": "database",
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19 "key": "string*",
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20 "database_name": "string*",
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21 "database_version": "string",
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22 "database_branch": "string",
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23 "database_commit": "string",
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24 "checksum_sha256": "char64"
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25 },
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26 "gene": {
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27 "type": "gene",
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28 "key": "string*",
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29 "name": "string*",
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30 "identity": "percentage",
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31 "alignment_length": "integer",
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32 "ref_gene_lenght": "integer",
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33 "coverage": "percentage",
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34 "depth": "float",
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35 "ref_id": "string*",
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36 "ref_acc": "string",
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37 "ref_start_pos": "integer",
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38 "ref_end_pos": "integer",
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39 "query_id": "string",
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40 "query_start_pos": "integer",
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41 "query_end_pos": "integer",
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42 "phenotypes": "array phenotype.key",
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43 "ref_database": "database.key"
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44 },
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45 "seq_region": {
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46 "type": "seq_region",
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47 "key": "string*",
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48 "name": "string*",
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49 "gene": "bool_or_unknown",
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50 "identity": "percentage",
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51 "alignment_length": "integer",
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52 "ref_gene_lenght": "integer",
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53 "coverage": "percentage",
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54 "depth": "float",
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55 "ref_id": "string*",
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56 "ref_acc": "string",
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57 "ref_start_pos": "integer",
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58 "ref_end_pos": "integer",
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59 "query_id": "string",
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60 "query_start_pos": "integer",
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61 "query_end_pos": "integer",
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62 "phenotypes": "array phenotype.key",
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63 "ref_database": "database.key"
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64 },
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65 "seq_variation": {
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66 "type": "seq_variation",
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67 "key": "string*",
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68 "ref_id": "string*",
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69 "seq_var": "seq_var_string",
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70 "codon_change": "codon_change_string",
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71 "ref_codon": "nucleotides",
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72 "var_codon": "nucleotides",
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73 "ref_aa": "aminoacid_1_char",
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74 "var_aa": "aminoacid_1_char",
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75 "ref_start_pos": "integer",
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76 "ref_end_pos": "integer",
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77 "substitution": "bool",
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78 "insertion": "bool",
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79 "deletion": "bool",
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80 "ref_database": "database.key",
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81 "genes": "array gene.key",
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82 "phenotypes": "array phenotype.key"
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83 },
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84 "phenotype": {
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85 "type": "phenotype",
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86 "key": "string*",
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87 "category": "vocabulary*",
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88 "amr_classes": "array vocabulary",
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89 "amr_resistance": "vocabulary",
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90 "amr_resistant": "bool_or_unknown",
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91 "genes": "array gene.key",
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92 "seq_variations": "array seq_variation.key",
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93 "ref_database": "database.key"
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94 }
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95 }
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