{"$update": {"1166": {"$update": {"model_sequences": {"$update": {"sequence": {"6035": {"dna_sequence": {"partial": "0", "sequence": "ATGGCTGAATTACCTCAATCAAGAATAAATGAACGAAATATTACCAGTGAAATGCGTGAATCATTTTTAGATTATGCGATGAGTGTTATCGTTGCTCGTGCATTGCCAGATGTTCGTGACGGTTTAAAACCAGTACATCGTCGTATACTATATGGATTAAATGAACAAGGTATGACACCGGATAAATCATATAAAAAATCAGCACGTATCGTTGGTGACGTAATGGGTAAATATCACCCTCATGGTGACTCATCTATTTATGAAGCAATGGTACGTATGGCTCAAGATTTCAGTTATCGTTATCCGCTTGTTGATGGCCAAGGTAACTTTGGTTCAATGGATGGAGATGGCGCAGCAGCAATGCGTTATACTGAAGCGCGTATGACTAAAATCACACTTGAACTGTTACGTGATATTAATAAAGATACAATAGATTTTATCGATAACTATGATGGTAATGAAAGAGAGCCGTCAGTCTTACCTGCTCGATTCCCTAACTTATTAGCCAATGGTGCATCAGGTATCGCGGTAGGTATGGCAACGAATATTCCACCACATAACTTAACAGAATTAATCAATGGTGTACTTAGCTTAAGTAAGAACCCTGATATTTCAATTGCTGAGTTAATGGAGGATATTGAAGGTCCTGATTTCCCAACTGCTGGACTTATTTTAGGTAAGAGTGGTATTAGACGTGCATATGAAACAGGTCGTGGTTCAATTCAAATGCGTTCTCGTGCAGTTATTGAAGAACGTGGAGGCGGACGTCAACGTATTGTTGTCACTGAAATTCCTTTCCAAGTGAATAAGGCTCGTATGATTGAAAAAATTGCAGAGCTCGTTCGTGACAAGAAAATTGACGGTATCACTGATTTACGTGATGAAACAAGTTTACGTACTGGTGTGCGTGTCGTTATTGATGTGCGTAAGGATGCAAATGCTAGTGTCATTTTAAATAACTTATACAAACAAACACCTCTTCAAACATCATTTGGTGTGAATATGATTGCACTTGTAAATGGTAGACCGAAGCTTATTAATTTAAAAGAAGCGTTGGTACATTATTTAGAGCATCAAAAGACAGTTGTTAGAAGACGTACGCAATACAACTTACGTAAAGCTAAAGATCGTGCCCACATTTTAGAAGGATTACGTATCGCACTTGACCATATCGATGAAATTATTTCAACGATTCGTGAGTCAGATACAGATAAAGTTGCAATGGAAAGCTTGCAACAACGCTTCAAACTTTCTGAAAAACAAGCTCAAGCTATTTTAGACATGCGTTTAAGACGTCTAACAGGTTTAGAGAGAGACAAAATTGAAGCTGAATATAATGAGTTATTAAATTATATTAGTGAATTAGAAGCAATCTTAGCTGATGAAGAAGTGTTATTACAGTTAGTTAGAGATGAATTGACTGAAATTAGAGATCGTTTCGGTGATGATCGTCGTACAGAAATTCAATTAGGTGGATTTGAAAACTTAGAGGACGAAGACTTAATTCCAGAAGAACAAATAGTAATTACACTAAGCCATAATAACTACATTAAACGTTTGCCGGTATCTACATATCGTGCTCAAAACCGTGGTGGTCGTGGTGTTCAAGGTATGAATACATTGGAAGAAGATTTTGTCAGTCAATTGGTAACTTTAAGTACACATGACCATGTATTGTTCTTTACTAACAAAGGTCGTGTATACAAACTTAAAGGTTACGAAGTGCCTGAGTTATCAAGACAGTCTAAAGGTATTCCTGTAGTGAATGCTATTGAACTTGAAAATGATGAAGTCATTAGTACAATGATTGCTGTTAAAGACCTTGAAAGTGAAGACAACTTCTTAGTGTTTGCAACTAAACGTGGTGTCGTTAAACGTTCAGCATTAAGTAACTTCTCAAGAATAAATAGAAATGGTAAGATTGCGATTTCGTTCAGAGAAGATGATGAGTTAATTGCAGTTCGCTTAACAAGTGGTCAAGAAGATATCTTGATTGGTACATCACATGCATCATTAATTCGATTCCCTGAATCAACATTACGTCCTTTAGGCCGTACAGCAACGGGTGTGAAAGGTATTACACTTCGTGAAGGTGACGAAGTTGTAGGGCTTGATGTAGCTCATGCAAACAGTGTTGATGAAGTATTAGTAGTTACTGAAAATGGTTATGGTAAACGTACGCCAGTTAATGACTATCGCTTATCAAATCGTGGTGGTAAAGGTATTAAAACAGCTACGATTACTGAGCGTAATGGTAATGTTGTATGTATCACTACAGTAACTGGTGAAGAAGATTTAATGATTGTTACTAATGCAGGTGTCATTATTCGACTAGATGTTGCAGATATTTCTCAAAATGGTCGTGCAGCACAAGGTGTTCGCTTAATTCGCTTAGGTGATGATCAATTTGTTTCAACGGTTGCTAAAGTAAAAGAAGATGCAGAAGATGAAACGAATGAAGATGAGCAATCTACTTCAACTGTATCTGAAGATGGTACTGAACAACAACGTGAAGCGGTTGTAAATGATGAAACACCAGGAAATGCAATTCATACTGAAGTGATTGATTCAGAAGAAAATGATGAAGATGGACGTATTGAAGTAAGACAAGATTTCATGGATCGTGTTGAAGAAGATATACAACAATCATCAGATGAAGAATAA", "fmax": "9675", "accession": "NC_009641.1", "fmin": "7011", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus", "NCBI_taxonomy_id": "1279", "NCBI_taxonomy_cvterm_id": "37074"}, "protein_sequence": {"accession": "WP_000819088.1", "sequence": "MAELPQSRINERNITSEMRESFLDYAMSVIVARALPDVRDGLKPVHRRILYGLNEQGMTPDKSYKKSARIVGDVMGKYHPHGDSSIYEAMVRMAQDFSYRYPLVDGQGNFGSMDGDGAAAMRYTEARMTKITLELLRDINKDTIDFIDNYDGNEREPSVLPARFPNLLANGASGIAVGMATNIPPHNLTELINGVLSLSKNPDISIAELMEDIEGPDFPTAGLILGKSGIRRAYETGRGSIQMRSRAVIEERGGGRQRIVVTEIPFQVNKARMIEKIAELVRDKKIDGITDLRDETSLRTGVRVVIDVRKDANASVILNNLYKQTPLQTSFGVNMIALVNGRPKLINLKEALVHYLEHQKTVVRRRTQYNLRKAKDRAHILEGLRIALDHIDEIISTIRESDTDKVAMESLQQRFKLSEKQAQAILDMRLRRLTGLERDKIEAEYNELLNYISELEAILADEEVLLQLVRDELTEIRDRFGDDRRTEIQLGGFENLEDEDLIPEEQIVITLSHNNYIKRLPVSTYRAQNRGGRGVQGMNTLEEDFVSQLVTLSTHDHVLFFTNKGRVYKLKGYEVPELSRQSKGIPVVNAIELENDEVISTMIAVKDLESEDNFLVFATKRGVVKRSALSNFSRINRNGKIAISFREDDELIAVRLTSGQEDILIGTSHASLIRFPESTLRPLGRTATGVKGITLREGDEVVGLDVAHANSVDEVLVVTENGYGKRTPVNDYRLSNRGGKGIKTATITERNGNVVCITTVTGEEDLMIVTNAGVIIRLDVADISQNGRAAQGVRLIRLGDDQFVSTVAKVKEDAEDETNEDEQSTSTVSEDGTEQQREAVVNDETPGNAIHTEVIDSEENDEDGRIEVRQDFMDRVEEDIQQSSDEE"}}}}}}}, "2315": {"$update": {"model_sequences": {"$update": {"sequence": {"6039": {"dna_sequence": {"partial": "0", "sequence": "ATGACCAGCCTTGCGCATCATGCGACAGAAAACCGCTCTGTAGCCGAATTTACTGAACAGGCTTACTTGAATTATGCCATGTACGTCATTATGGACCGTGCATTGCCGCATATCAGTGATGGCTTAAAGCCCGTACAGCGCCGTATTGTCTATGCTATGAGCGAGCTAGGCTTAAAAAGCAGTGGCAAGCCAAAAAAATCAGCGCGTACAGTGGGTGATGTACTTGGTAAATACCACCCACATGGTGACTTGGCATGTTATGAAGCCATGGTACTCATGGCTCAGCCATTTAGTTACCGCTATCCTTTAATCGAAGGTCAGGGGAACTGGGGTTCACCAGATGATCCTAAATCTTTTGCTGCGATGCGTTATACCGAAGCCAAACTCTCGGCTTATAGTGAATTATTGCTGAGCGAATTAGGTCAGGGCACTAGCGAATGGCAAGATAACTTTGATGGTTCTTTAAAAGAACCGATCACTTTACCTGCACGTGTACCTAATATTCTTCTTAATGGTACGACAGGTATTGCTGTCGGGATGGCAACTGATATCCCGCCACATAATTTGCGTGAAGTTGTAAAAGGCACAATTGCTTTAATCCGTAATCCGCAAACCTCGGACGAAAAATTAGCTGAATATATTCCGGCTCCGGATTTACCAACCAAAGCTGAAATTATTACCCCGCCAGAAGAATTACTCAAAATCCAGACCACTGGTCGTGGTAGTTACCGTATGCGAGCGGTATATACCATTGAGAAAAATGAAATCGTAATTACTGAGCTGCCATATCAAGTCTCTGGTTCTAAGGTAATTACTCAAATTGCTGACCAGATGCAGGCTAAAAAGCTGCCATTAGTCGTTGATGTGCGTGATGAATCGGATCATGAAAACCCGACACGACTCGTGATTGTACTGCGCTCTAACCGTATTGATGCGGAAGCAGTAATGAGTCACTTATTTGCGACCACCGATTTAGAATCAAGCTATCGTGTCAATTTAAACATGATTGGCGAAGATGGCCGTCCTCAGGTGAAATCAATTCGTCGTATTTTGCTTGAATGGATCGAGATCCGTAAAAAAACGGTAACTCGTCGTTTGCAGTACCATTTAAACCGTATTGAAAAGCGCCTGCATATTTTGGCAGGTCTTTTAATTGCTTATCTCGATATTGATACAGTCATTCGTATTATTCGTGAAGAAGACCAGCCTAAGCCAGTCTTGATGGAACACTTTAATATTGATGAGATACAGGCCGAGGCGATTTTAGAGCTTAAATTACGTCATTTGGCAAAGCTTGAAGAGATGGAAATTCGTCATGAACAAGATGAGCTTTCCGCGAAAGCTGCCATTATTCGTGAACAACTCGAAAATCCTGAATCTTTAAAAAATTTGATTATTGGCGAATTAAAAGAAGATGCGAAAAAGTTCGGTGATGAGCGCCGTTCTCCAATTGTTGCACGTGCTGAAGCGGTTCAAATTAAAGAACAGGATTTAATGCCAGCTGAAACGGTAACAGTCGTGTTGTCTGAAGCAGGCTGGGTTCGTGCGGCAAAAGGTGCGGATGTGGATGCTGAAAATCTGAACTACCGTGCTGGGGACCAATATTTAAGTCATGCTGTCGGGAAAACCAATCAGCGAGTTTACTTCCTTGATGAAACAGGGCGCAGCTATGCCTTGCCAATTAGTAACTTACCTTCAGCGAGAGGCTTGGGGGATCCATTAAGTTCTAAATTATCACCAGCAAGTGGCGTATCGTTTATTCAGGTTTATTTAGATGATGATGAGTCTGAGTTGATTGCTGCAAGTTCGGCAGGTTATGGTTTTAAAACGCAAACCAAGCAATTAGATACCAATGCGAAAGCCGGTAAGACATTCTTAACGGTTCCGGATAAGGCAAAGGCTTTACCACTTATTTCTGCCCAAAACATGACGCATTTGGCTGTACTGAGCTCAGCAGGGCGTTTGTTAATTTTAGATTTGGCAGAACTACCAAATTTAAATAAAGGTAAAGGTAATAAGTTGATACAACTTGAAGGCAAAGAGCAAATTTTATCCATGACAACCCTGAACTTAGATGAAATAATTCAGGTGGTTGCAGGTCAACAACATCTCAAATTAAAAGGTGATGATCTACAAAAATACATGGGTAAACGTGCTTCGAAAGGTCAGCTCTTACCACGTGGATATCAAAAAGCAAATAAACTGTTGATTCAGAGATAA", "fmax": "3047346", "accession": "NZ_CP009257.1", "fmin": "3045126", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter", "NCBI_taxonomy_id": "469", "NCBI_taxonomy_cvterm_id": "37046"}, "protein_sequence": {"accession": "WP_000202252.1", "sequence": "MTSLAHHATENRSVAEFTEQAYLNYAMYVIMDRALPHISDGLKPVQRRIVYAMSELGLKSSGKPKKSARTVGDVLGKYHPHGDLACYEAMVLMAQPFSYRYPLIEGQGNWGSPDDPKSFAAMRYTEAKLSAYSELLLSELGQGTSEWQDNFDGSLKEPITLPARVPNILLNGTTGIAVGMATDIPPHNLREVVKGTIALIRNPQTSDEKLAEYIPAPDLPTKAEIITPPEELLKIQTTGRGSYRMRAVYTIEKNEIVITELPYQVSGSKVITQIADQMQAKKLPLVVDVRDESDHENPTRLVIVLRSNRIDAEAVMSHLFATTDLESSYRVNLNMIGEDGRPQVKSIRRILLEWIEIRKKTVTRRLQYHLNRIEKRLHILAGLLIAYLDIDTVIRIIREEDQPKPVLMEHFNIDEIQAEAILELKLRHLAKLEEMEIRHEQDELSAKAAIIREQLENPESLKNLIIGELKEDAKKFGDERRSPIVARAEAVQIKEQDLMPAETVTVVLSEAGWVRAAKGADVDAENLNYRAGDQYLSHAVGKTNQRVYFLDETGRSYALPISNLPSARGLGDPLSSKLSPASGVSFIQVYLDDDESELIAASSAGYGFKTQTKQLDTNAKAGKTFLTVPDKAKALPLISAQNMTHLAVLSSAGRLLILDLAELPNLNKGKGNKLIQLEGKEQILSMTTLNLDEIIQVVAGQQHLKLKGDDLQKYMGKRASKGQLLPRGYQKANKLLIQR"}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_value": {"9874": "D105E", "9872": "S84L", "9873": "V104I"}, "clinical": {"9874": "D105E", "9872": "S84L", "9873": "V104I"}}}}}}}, "212": {"$update": {"model_sequences": {"$update": {"sequence": {"6038": {"dna_sequence": {"partial": "0", "sequence": "GTGAGTGAAATAATTCAAGATTTATCACTTGAAGATGTTTTAGGTGATCGCTTTGGAAGATATAGTAAATATATTATTCAAGAGCGTGCATTGCCAGATGTTCGTGATGGTTTAAAACCAGTACAACGTCGTATTTTATATGCAATGTATTCAAGTGGTAATACACACGATAAAAATTTCCGTAAAAGTGCGAAAACAGTCGGTGATGTTATTGGTCAATATCATCCACATGGAGACTCCTCAGTGTACGAAGCAATGGTCCGTTTAAGTCAAGACTGGAAGTTACGACATGTCTTAATAGAAATGCATGGTAATAATGGTAGTATCGATAATGATCCGCCAGCGGCAATGCGTTACACTGAAGCTAAGTTAAGCTTACTAGCTGAAGAGTTATTACGTGATATTAATAAAGAGACAGTTTCTTTCATTCCAAACTATGATGATACGACACTCGAACCAATGGTATTGCCATCAAGATTTCCTAACTTACTAGTGAATGGTTCTACAGGTATATCTGCAGGTTACGCGACAGATATACCACCACATAATTTAGCTGAAGTGATTCAAGCAACACTTAAATATATTGATAATCCGGATATTACAGTCAATCAATTAATGAAATATATTAAAGGTCCTGATTTTCCAACTGGTGGTATTATTCAAGGTATTGATGGTATTAAAAAAGCTTATGAATCAGGTAAAGGTAGAATTATAGTTCGTTCTAAAGTTGAAGAAGAAACTTTACGCAATGGACGTAAACAGTTAATTATTACTGAAATTCCATATGAAGTGAACAAAAGTAGCTTAGTAAAACGTATCGATGAATTACGTGCTGACAAAAAAGTCGATGGTATCGTTGAAGTACGTGATGAAACTGATAGAACTGGTTTACGAATAGCAATTGAATTGAAAAAAGATGTGAACAGTGAATCAATCAAAAATTATCTTTATAAAAACTCTGATTTACAGATTTCATATAATTTCAACATGGTCGCTATTAGTGATGGTCGTCCAAAATTGATGGGTATTCGTCAAATTATAGATAGTTATTTGAATCACCAAATTGAGGTTGTTGCAAATAGAACGAAGTTTGAATTAGATAATGCAGAAAAACGTATGCATATCGTTGAAGGTTTGATTAAAGCGTTGTCAATTTTAGATAAAGTAATCGAATTGATTCGTAGCTCTAAAAACAAGCGTGACGCTAAAGAAAACCTTATCGAAGTATACGAGTTCACAGAAGAACAGGCTGAAGCAATTGTAATGTTACAGTTATATCGTTTAACAAATACTGACATAGTTGCGCTTGAAGGTGAACATAAAGAACTTGAAGCATTAATCAAACAATTACGTCATATTCTTGATAACCATGATGCATTATTGAATGTCATAAAAGAAGAATTGAATGAAATTAAAAAGAAATTCAAATCTGAACGACTGTCTTTAATTGAAGCAGAAATTGAAGAAATTAAAATTGACAAAGAAGTTATGGTGCCTAGTGAAGAAGTTATTTTAAGTATGACACGTCATGGATATATTAAACGTACTTCTATTCGTAGCTTTAATGCTAGCGGTGTTGAAGATATTGGTTTAAAAGATGGTGACAGTTTACTTAAACATCAAGAAGTAAATACGCAAGATACCGTACTAGTATTTACAAATAAAGGTCGTTATCTATTTATACCGGTTCATAAATTAGCAGATATTCGTTGGAAAGAATTGGGACAACATGTATCACAAATAGTTCCTATCGAAGAAGATGAAGTGGTTATTAATGTCTTTAATGAAAAGGACTTTAATACAGATGCATTTTATGTTTTTGCGACTCAAAATGGCATGATTAAGAAAAGTACAGTGCCTCTATTTAAAACAACGCGTTTTAATAAACCTTTAATTGCTACTAAAGTTAAAGAAAATGATGATTTGATTAGTGTTATGCGCTTTGAAAAAGATCAATTAATTACCGTCATTACTAATAAAGGTATGTCATTAACGTATAATACAAGTGAACTATCAGATACCGGATTAAGGGCAGCTGGTGTTAAATCAATAAATCTTAAAGCTGAAGATTTCGTTGTTATGACAGAAGGTGTTTCTGAAAATGATACTATATTGATGGCCACACAACGCGGCTCGTTAAAACGTATTAGTTTTAAAATCTTACAAGTTGCTAAAAGAGCACAACGTGGAATAACTTTATTAAAAGAATTAAAGAAAAATCCACATCGTATTGTAGCTGCACATGTAGTGACAGGTGAACATAGTCAATATACATTATATTCAAAATCAAATGAAGAACATGGTTTAATTAATGATATTCATAAATCTGAACAATATACAAATGGCTCATTCATTGTAGATACAGATGATTTTGGTGAAGTAATAGACATGTATATTAGCTAA", "fmax": "1400372", "accession": "NC_002951.2", "fmin": "1397969", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Staphylococcus", "NCBI_taxonomy_id": "1279", "NCBI_taxonomy_cvterm_id": "37074"}, "protein_sequence": {"accession": "WP_001289569.1", "sequence": "MSEIIQDLSLEDVLGDRFGRYSKYIIQERALPDVRDGLKPVQRRILYAMYSSGNTHDKNFRKSAKTVGDVIGQYHPHGDSSVYEAMVRLSQDWKLRHVLIEMHGNNGSIDNDPPAAMRYTEAKLSLLAEELLRDINKETVSFIPNYDDTTLEPMVLPSRFPNLLVNGSTGISAGYATDIPPHNLAEVIQATLKYIDNPDITVNQLMKYIKGPDFPTGGIIQGIDGIKKAYESGKGRIIVRSKVEEETLRNGRKQLIITEIPYEVNKSSLVKRIDELRADKKVDGIVEVRDETDRTGLRIAIELKKDVNSESIKNYLYKNSDLQISYNFNMVAISDGRPKLMGIRQIIDSYLNHQIEVVANRTKFELDNAEKRMHIVEGLIKALSILDKVIELIRSSKNKRDAKENLIEVYEFTEEQAEAIVMLQLYRLTNTDIVALEGEHKELEALIKQLRHILDNHDALLNVIKEELNEIKKKFKSERLSLIEAEIEEIKIDKEVMVPSEEVILSMTRHGYIKRTSIRSFNASGVEDIGLKDGDSLLKHQEVNTQDTVLVFTNKGRYLFIPVHKLADIRWKELGQHVSQIVPIEEDEVVINVFNEKDFNTDAFYVFATQNGMIKKSTVPLFKTTRFNKPLIATKVKENDDLISVMRFEKDQLITVITNKGMSLTYNTSELSDTGLRAAGVKSINLKAEDFVVMTEGVSENDTILMATQRGSLKRISFKILQVAKRAQRGITLLKELKKNPHRIVAAHVVTGEHSQYTLYSKSNEEHGLINDIHKSEQYTNGSFIVDTDDFGEVIDMYIS"}}}}}}}, "489": {"$update": {"model_param": {"$insert": {"43012": {"param_value": {"9843": "L16R"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}, "43011": {"param_value": {"9841": "E92D"}, "param_type_id": "43011", "param_type": "Minimal Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as minimal confidence has a minimal association of the mutation with phenotypic drug resistance. There is inconclusive evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 1 but less or equal to 5."}, "42998": {"param_value": {"9842": "R118fs", "9840": "L79S"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}}}}}, "1176": {"$update": {"model_param": {"$insert": {"43013": {"param_value": {"9553": "V469L"}, "param_type_id": "43013", "param_type": "Indeterminate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as indeterminate means that there is no statistically significant threshold reached and additional data is required. LR is indeterminate."}, "42998": {"param_value": {"9560": "I317V", "9558": "S315R", "9555": "W191R", "9554": "T667P", "9557": "S315T", "9556": "S315N"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43011": {"param_value": {"9552": "R463L"}, "param_type_id": "43011", "param_type": "Minimal Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as minimal confidence has a minimal association of the mutation with phenotypic drug resistance. There is inconclusive evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 1 but less or equal to 5."}}}}}, "2291": {"$update": {"ARO_category": {"$update": {"39245": {"$update": {"category_aro_name": "antibiotic-resistant murA transferase"}}}}}}, "196": {"$update": {"ARO_category": {"$delete": ["39310"], "$insert": {"36374": {"category_aro_name": "ethambutol resistant embB", "category_aro_cvterm_id": "36374", "category_aro_accession": "3000235", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "embB gene encodes for an arabinosyl transferase in the arabinogalactan synthesis pathway. It is inhibited by ethambutol. Mutations within the ERDR region of embB confers resistance to ethambutol."}}}, "model_param": {"$insert": {"43010": {"param_value": {"9473": "G406A", "9467": "D354A", "9466": "S347I", "9470": "G406S", "9485": "M306I"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}, "43013": {"param_value": {"9478": "N13S", "9480": "R213Q"}, "param_type_id": "43013", "param_type": "Indeterminate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as indeterminate means that there is no statistically significant threshold reached and additional data is required. LR is indeterminate."}, "42998": {"param_value": {"9469": "L402V", "9471": "G406C", "9476": "Q497R", "9474": "A454T", "9465": "Y334H", "9489": "F330S", "9488": "D328Y", "9482": "N296H", "9481": "S22C", "9487": "Y319C", "9486": "Y319S", "9484": "M306V"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43011": {"param_value": {"9472": "G406D", "9483": "M306L", "9477": "D1024N", "9475": "Q497K"}, "param_type_id": "43011", "param_type": "Minimal Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as minimal confidence has a minimal association of the mutation with phenotypic drug resistance. There is inconclusive evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 1 but less or equal to 5."}, "43012": {"param_value": {"9479": "L172R", "9468": "E378A"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}}}}}, "2297": {"$update": {"ARO_category": {"$insert": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}}}}, "2296": {"$update": {"ARO_category": {"$insert": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}}}}, "1203": {"$update": {"model_param": {"$insert": {"43013": {"param_value": {"9586": "-nt-134:G", "9584": "G313R", "9585": "-nt-132:G"}, "param_type_id": "43013", "param_type": "Indeterminate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as indeterminate means that there is no statistically significant threshold reached and additional data is required. LR is indeterminate."}, "42998": {"param_value": {"9582": "-nt-134:G"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43011": {"param_value": {"9583": "R268H"}, "param_type_id": "43011", "param_type": "Minimal Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as minimal confidence has a minimal association of the mutation with phenotypic drug resistance. There is inconclusive evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 1 but less or equal to 5."}, "43012": {"param_value": {"9581": "-nt-132:G"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}}}}}, "660": {"$update": {"model_sequences": {"$update": {"sequence": {"6037": {"dna_sequence": {"partial": "0", "sequence": "TTGTATCTTATGTCTAACATTCAAAACATGTCCCTGGAGGACATCATGGGAGAGCGCTTTGGTCGCTACTCCAAGTACATTATTCAAGACCGGGCTTTGCCAGATATTCGTGATGGGTTGAAGCCGGTTCAACGCCGTATTCTTTATTCTATGAATAAGGATAGCAATACTTTTGACAAGAGCTACCGTAAGTCGGCCAAGTCAGTCGGGAACATCATGGGGAATTTCCACCCACACGGGGATTCTTCTATCTATGATGCCATGGTTCGTATGTCACAGAACTGGAAAAATCGTGAGATTCTAGTTGAAATGCACGGTAATAACGGTTCTATGGACGGAGATCCTCCTGCGGCTATGCGTTATACTGAGGCACGTTTGTCTGAAATTGCAGGCTACCTTCTTCAGGATATCGAGAAAAAGACAGTTCCTTTTGCATGGAACTTTGACGATACGGAGAAAGAACCAACGGTCTTGCCAGCAGCCTTTCCAAACCTCTTGGTCAATGGTTCGACTGGGATTTCGGCTGGTTATGCCACAGACATTCCTCCCCATAATTTAGCTGAGGTCATAGATGCTGCAGTTTACATGATTGACCACCCAACTGCAAAGATTGATAAACTCATGGAATTCTTACCTGGACCAGACTTCCCTACAGGGGCTATTATTCAGGGTCGTGATGAAATCAAGAAAGCCTATGAGACTGGGAAAGGGCGCGTGGTTGTTCGTTCCAAGACTGAAATTGAAAAGCTAAAAGGTGGTAAGGAACAAATCGTTATTACTGAGATTCCTTATGAAATCAATAAGGCCAATCTAGTCAAGAAAATCGATGATGTTCGTGTTAATAACAAGGTAGCTGGGATTGCTGAGGTTCGTGATGAGTCTGACCGTGATGGTCTTCGTATCGCTATTGAACTTAAGAAAGACGCTAATACTGAGCTTGTTCTCAACTACTTATTTAAGTACACCGACCTACAAATCAACTACAACTTTAATATGGTGGCGATTGACAATTTCACACCTCGTCAGGTTGGGATTGTTCCAATCCTGTCTAGCTACATCGCTCACCGTCGAGAAGTGATTTTGGCGCGTTCACGCTTTGACAAAGAAAAGGCTGAGAAACGTCTCCGTATCGTCGAAGGTTTGATTCGTGTGATTTCGATTTTGGATGAAGTCATTGCTCTTATCCGTGCTTCTGAGAATAAGGCGGACGCCAAGGAAAACCTCAAAGTTAGCTATGATTTTACGGAAGAACAGGCTGAGGCTATCGTAACTTTGCAACTGTACCGTTTGACCAATACCGATGTGGTTGTCTTGCAGGAAGAAGAAGCAGAGCTTCGTGAGAAGATTGCTATGCTGGCGGCTATTATCGGTGATGAAAGGACTATGTACAATCTCATGAAGAAAGAACTTCGTGAGGTCAAGAAGAACTTTGCAACTCCTCGTTTGAGTTCTTTAGAAGACACTGCGAAAGCAATTGAGATTGATACAGCTAGTCTTATCGCTGAGGAAGATACCTACGTCAGCGTGACCAAGGCAGGTTACATCAAGCGTACCAGTCCACGTTCCTTTGCGGCTTCCACCTTGGAAGAAATTGGCAAGCGTGATGATGACCGTTTGATTTTTGTTCAATCTGCCAAGACAACCCAGCACCTCTTGATGTTCACAAGTCTTGGAAATGTCATCTACAGACCAATCCATGAGTTGGCAGATATTCGTTGGAAGGACATCGGAGAGCATCTGAGCCAAACCATCACAAACTTTGAAACGAATGAAGCAATCCTTTATGTGGAAGTACTGGATCAGTTTGACGATGCGACAACCTACTTTGCAGCGACTCGCCTTGGTCAAATCAAACGGGTAGAGCGAAAAGAATTCACTCCATGGCGGACCTATAGATCTAAGTCTGTCAAGTATGCTAAGCTCAAAGACGATACAGATCAGATTGTAGCAGTGGCTCCGATTAAACTAGATGATGTTGTCTTGGTTAGTCAAAATGGTTATGCCCTGCGTTTCAATATCGAAGAGGTTCCGGTTGTCGGTGCTAAGGCAGCAGGTGTCAAGGCTATGAATTTGAAAGAAGATGATGTCCTCCAATCTGGCTTTATCTGTAATACTTCGTCCTTCTACCTCTTGACCCAGCGTGGAAGCTTGAAACGTGTTTCCATTGAGGAAATTCTAGCAACCAGCCGTGCCAAACGAGGATTACAAGTCTTGCGTGAGTTGAAAAACAAACCGCATCGTGTCTTCTTGGCAGGAGCAGTTGCAGAGCAAGGATTTGTTGGCGATTTCTTCAGTACGGAAGTGGATGTGAACGACCAAACTCTGCTTGTCCAATCCAATAAAGGAACAATCTATGAAAGCCGATTGCAAGACTTGAACTTGTCAGAACGCACTAGCAATGGAAGCTTCATTTCTGACACGATTTCAGATGAAGAAGTTTTTGACGCTTATCTTCAGGAAGTAGTTACTGAAGATAAATAA", "fmax": "754721", "accession": "NC_003098.1", "fmin": "752240", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Streptococcus pneumoniae R6", "NCBI_taxonomy_id": "171101", "NCBI_taxonomy_cvterm_id": "39596"}, "protein_sequence": {"accession": "NP_358351.1", "sequence": "MYLMSNIQNMSLEDIMGERFGRYSKYIIQDRALPDIRDGLKPVQRRILYSMNKDSNTFDKSYRKSAKSVGNIMGNFHPHGDSSIYDAMVRMSQNWKNREILVEMHGNNGSMDGDPPAAMRYTEARLSEIAGYLLQDIEKKTVPFAWNFDDTEKEPTVLPAAFPNLLVNGSTGISAGYATDIPPHNLAEVIDAAVYMIDHPTAKIDKLMEFLPGPDFPTGAIIQGRDEIKKAYETGKGRVVVRSKTEIEKLKGGKEQIVITEIPYEINKANLVKKIDDVRVNNKVAGIAEVRDESDRDGLRIAIELKKDANTELVLNYLFKYTDLQINYNFNMVAIDNFTPRQVGIVPILSSYIAHRREVILARSRFDKEKAEKRLRIVEGLIRVISILDEVIALIRASENKADAKENLKVSYDFTEEQAEAIVTLQLYRLTNTDVVVLQEEEAELREKIAMLAAIIGDERTMYNLMKKELREVKKNFATPRLSSLEDTAKAIEIDTASLIAEEDTYVSVTKAGYIKRTSPRSFAASTLEEIGKRDDDRLIFVQSAKTTQHLLMFTSLGNVIYRPIHELADIRWKDIGEHLSQTITNFETNEAILYVEVLDQFDDATTYFAATRLGQIKRVERKEFTPWRTYRSKSVKYAKLKDDTDQIVAVAPIKLDDVVLVSQNGYALRFNIEEVPVVGAKAAGVKAMNLKEDDVLQSGFICNTSSFYLLTQRGSLKRVSIEEILATSRAKRGLQVLRELKNKPHRVFLAGAVAEQGFVGDFFSTEVDVNDQTLLVQSNKGTIYESRLQDLNLSERTSNGSFISDTISDEEVFDAYLQEVVTEDK"}}}}}, "model_param": {"$update": {"snp": {"$update": {"param_value": {"9865": "S82Y", "9867": "D86H", "9866": "S82F"}, "clinical": {"9865": "S82Y", "9867": "D86H", "9866": "S82F"}}, "$delete": ["experimental"]}}}}}, "2820": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"$delete": ["8718", "7938", "8721", "8719"], "$insert": {"9887": "T2663C", "9886": "A2109G", "9885": "A2107G", "9884": "A2107C"}}, "clinical": {"$delete": ["8718", "7938", "8721", "8719"], "$insert": {"9887": "T2663C", "9886": "A2109G", "9885": "A2107G", "9884": "A2107C"}}}}}}}}, "3308": {"$update": {"ARO_description": "A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.", "ARO_category": {"$delete": ["35921", "35999"], "$insert": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}}}}, "2092": {"$update": {"model_param": {"$update": {"40494": {"$update": {"param_description": "A frameshift is a type of genetic mutation caused by a nucleotide insertion or deletion that does not equal 3 bases. This changes the grouping of codons and thus the reading frame during translation, resulting in an incomplete or inactive protein product. Many frameshift mutations generate downstream STOP codons, resulting in premature peptide translation termination. Frameshifts may also confer antibiotic resistance through partial or total protein loss-of-function. Frameshift mutations are included with relevant models when applicable, with the following notation: [wild-type AA][position]fs;[[wild-type AA][position]STOP], where AA is an amino acid. If the premature STOP codon position is unknown or does not exist, [wild-type AA][position]fs is sufficient. Termination can also be denoted as: Ter[position]fs. This parameter is currently not included in detection algorithms."}}}}}}, "100": {"$update": {"model_param": {"$insert": {"42998": {"param_value": {"9508": "Y147STOP", "9506": "P422fs", "9507": "G11fs", "9504": "T342K", "9505": "N379D", "9511": "A-11G", "9510": "H281P"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43012": {"param_value": {"9509": "S266R"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}}}}}, "2800": {"$update": {"ARO_category": {"$delete": ["36218", "35936", "35919", "35945"]}}}, "3302": {"$update": {"ARO_description": "A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.", "ARO_category": {"$delete": ["35921", "35999"], "$insert": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}}}}, "3651": {"$update": {"model_param": {"$insert": {"42998": {"param_value": {"9446": "G1484T", "9445": "A1401G"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43010": {"param_value": {"9447": "A514C"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}}}}}, "3292": {"$update": {"ARO_description": "A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.", "ARO_category": {"$delete": ["35921", "35999"], "$insert": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}}}}, "3293": {"$update": {"ARO_description": "A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.", "ARO_category": {"$delete": ["35921", "35999"], "$insert": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}}}}, "1574": {"$update": {"ARO_category": {"$update": {"43060": {"$update": {"category_aro_name": "isoniazid resistant inhA"}}}}, "model_param": {"$insert": {"43013": {"param_value": {"9857": "T-8A"}, "param_type_id": "43013", "param_type": "Indeterminate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as indeterminate means that there is no statistically significant threshold reached and additional data is required. LR is indeterminate."}, "42998": {"param_value": {"9550": "I194T", "9855": "T280G", "9856": "C-15T", "9549": "T162S"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43011": {"param_value": {"9548": "S94A"}, "param_type_id": "43011", "param_type": "Minimal Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as minimal confidence has a minimal association of the mutation with phenotypic drug resistance. There is inconclusive evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 1 but less or equal to 5."}, "43010": {"param_value": {"9858": "T-8C"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}}}}}, "3348": {"$update": {"ARO_category": {"$delete": ["35945", "35919"]}}}, "3701": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"9878": "R228S"}, "clinical": {"9878": "R228S"}}}}}}}, "696": {"$update": {"ARO_category": {"$delete": ["36218", "35919"]}}}, "851": {"$update": {"model_param": {"$insert": {"43010": {"param_value": {"9665": "H71R", "9682": "V128G"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}, "42998": {"param_value": {"9673": "T100P", "9652": "P54L", "9653": "H57D", "9650": "I5T", "9651": "H51R", "9656": "F58S", "9657": "I6T", "9672": "G97S", "9655": "H57R", "9658": "P62S", "9659": "D63G", "9678": "T114fs", "9679": "L116R", "9670": "D8E", "9691": "Q141P", "9689": "C138R", "9688": "C14R", "9681": "D12A", "9680": "L117fs", "9683": "V131fs", "9685": "T135P", "9684": "I133T", "9687": "D136fs", "9686": "D136Y", "9667": "D8N", "9666": "T76P", "9664": "V7G", "9663": "P69R", "9662": "W68G", "9661": "W68R", "9660": "S67P", "9700": "L182S", "9647": "L4S", "9646": "Y34D", "9669": "H82R", "9668": "D8H", "9674": "Q10P", "9702": "A-11G", "9675": "Q10R", "9692": "A146E", "9676": "Y103STOP", "9648": "D49N", "9677": "G108STOP", "9698": "V180A", "9699": "V180G", "9696": "M175V", "9697": "V180F", "9694": "L151S", "9695": "S164STOP", "9649": "D49G", "9693": "A146V", "9690": "V139G", "9671": "L85R"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43011": {"param_value": {"9701": "A-11C"}, "param_type_id": "43011", "param_type": "Minimal Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as minimal confidence has a minimal association of the mutation with phenotypic drug resistance. There is inconclusive evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 1 but less or equal to 5."}, "43012": {"param_value": {"9703": "G-1319A", "9654": "I6L"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}}}}}, "2131": {"$update": {"model_param": {"$insert": {"43012": {"param_value": {"9847": "C492T"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}, "42998": {"param_value": {"9849": "C517T", "9848": "A514C"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43010": {"param_value": {"9846": "A1401G"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}}}}}, "3290": {"$update": {"ARO_description": "A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.", "ARO_category": {"$delete": ["35921", "35999"], "$insert": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}}}}, "953": {"$update": {"ARO_category": {"$insert": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}}}}, "1197": {"$update": {"ARO_category": {"$update": {"40003": {"$update": {"category_aro_name": "antibiotic-resistant rpsL"}}}}, "model_param": {"$insert": {"42998": {"param_value": {"9845": "K88R", "9844": "K43R"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}}}}}, "2381": {"$update": {"ARO_category": {"$update": {"41412": {"$update": {"category_aro_name": "antibiotic-resistant UhpT"}}}}}}, "2380": {"$update": {"ARO_category": {"$update": {"41411": {"$update": {"category_aro_name": "antibiotic-resistant GlpT"}}}}}}, "3289": {"$update": {"ARO_description": "A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.", "ARO_category": {"$delete": ["35921", "35999"], "$insert": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}}}}, "3300": {"$update": {"ARO_category": {"$delete": ["35919"]}}}, "2386": {"$update": {"ARO_category": {"$delete": ["36218", "35919"]}}}, "2070": {"$update": {"model_param": {"$insert": {"43010": {"param_value": {"9442": "A514C"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}, "43012": {"param_value": {"9443": "C517T", "9441": "C492T"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}, "42998": {"param_value": {"9439": "A1401G", "9440": "G1484T"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}}}}}, "571": {"$update": {"ARO_category": {"$delete": ["36218", "35919"]}}}, "3628": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"$delete": ["9298", "9297"]}, "clinical": {"$delete": ["9298", "9297"]}}}}}}}, "632": {"$update": {"ARO_category": {"$insert": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}}}}, "1237": {"$update": {"model_param": {"$insert": {"43010": {"param_value": {"9776": "H445L", "9786": "P45S"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}, "43013": {"param_value": {"9798": "E250G"}, "param_type_id": "43013", "param_type": "Indeterminate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as indeterminate means that there is no statistically significant threshold reached and additional data is required. LR is indeterminate."}, "42998": {"param_value": {"9780": "M434I", "9743": "H445Y", "9775": "H445D", "9742": "S450L", "9784": "H445Y", "9794": "H835R", "9782": "D435G", "9793": "R827H", "9792": "L731P", "9791": "F503S", "9783": "D435V", "9797": "I1106T", "9785": "H445R", "9795": "G836S", "9787": "S450W", "9788": "P45L", "9779": "Q432P", "9777": "S450L", "9790": "I480V", "9796": "Q975H"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43011": {"param_value": {"9781": "D435Y", "9778": "L430P", "9789": "L452P"}, "param_type_id": "43011", "param_type": "Minimal Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as minimal confidence has a minimal association of the mutation with phenotypic drug resistance. There is inconclusive evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 1 but less or equal to 5."}, "43012": {"param_value": {"9799": "C-61T"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}}}}}, "1339": {"$update": {"ARO_category": {"$delete": ["39310"], "$insert": {"40047": {"category_aro_name": "ethambutol resistant embR", "category_aro_cvterm_id": "40047", "category_aro_accession": "3003454", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Mutations that occurs on the embR genes resulting in the resistance to ethambutol"}}}, "model_param": {"$insert": {"43012": {"param_value": {"9494": "C372G", "9495": "F376L", "9496": "C110Y", "9497": "C-207G"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}}}}}, "756": {"$update": {"ARO_category": {"$insert": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}}}}, "3745": {"$update": {"model_param": {"$insert": {"43012": {"param_value": {"9444": "C344T"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}}}}}, "2284": {"$update": {"ARO_category": {"$update": {"39245": {"$update": {"category_aro_name": "antibiotic-resistant murA transferase"}}}}}}, "2285": {"$update": {"ARO_category": {"$update": {"39245": {"$update": {"category_aro_name": "antibiotic-resistant murA transferase"}}}}}}, "2286": {"$update": {"ARO_category": {"$update": {"39245": {"$update": {"category_aro_name": "antibiotic-resistant murA transferase"}}}}}}, "1354": {"$update": {"ARO_category": {"$delete": ["39310"], "$insert": {"40045": {"category_aro_name": "ethambutol resistant embA", "category_aro_cvterm_id": "40045", "category_aro_accession": "3003452", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Mutations that occurs on the embA genes resulting in the resistance to ethambutol"}}}, "model_param": {"$insert": {"43010": {"param_value": {"9461": "C-16T"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}, "43012": {"param_value": {"9455": "P913S", "9456": "V206M"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}, "42998": {"param_value": {"9458": "C-12T", "9459": "C-16A", "9457": "C-11A", "9464": "C-8T", "9460": "C-16G", "9463": "C-4A", "9462": "G-43C"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}}}}}, "2374": {"$update": {"ARO_category": {"$update": {"41412": {"$update": {"category_aro_name": "antibiotic-resistant UhpT"}}}}}}, "3403": {"$update": {"model_param": {"$insert": {"42998": {"param_value": {"9719": "A381V", "9722": "Ter482fs", "9720": "A412V", "9721": "A440T"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}}}}}, "2276": {"$update": {"ARO_category": {"$update": {"36585": {"$update": {"category_aro_name": "antibiotic-resistant isoleucyl-tRNA synthetase (ileS)"}}}}}}, "2278": {"$update": {"ARO_category": {"$update": {"36585": {"$update": {"category_aro_name": "antibiotic-resistant isoleucyl-tRNA synthetase (ileS)"}}}}}}, "2295": {"$update": {"ARO_category": {"$insert": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}}}}, "1935": {"$update": {"model_param": {"$insert": {"43010": {"param_value": {"9627": "S91P", "9613": "D94A"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}, "42998": {"param_value": {"9603": "D94N", "9605": "D94G", "9604": "D94Y", "9610": "A90V", "9606": "D94Y", "9609": "G88C", "9612": "D94H", "9611": "D94N", "9614": "D94G", "9628": "D94H", "9623": "D94G", "9622": "D94A", "9621": "D94Y", "9620": "D94N", "9626": "A90V", "9625": "D89N"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43012": {"param_value": {"9608": "G668D", "9607": "S95T", "9624": "A384V"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}}}}}, "127": {"$update": {"ARO_category": {"$delete": ["36218", "35919"]}}}, "3287": {"$update": {"ARO_description": "A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.", "ARO_category": {"$delete": ["35921", "35999"], "$insert": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}}}}, "2132": {"$update": {"model_param": {"$insert": {"42998": {"param_value": {"9599": "A1401G"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}, "43011": {"param_value": {"9601": "C517T", "9600": "A514C"}, "param_type_id": "43011", "param_type": "Minimal Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as minimal confidence has a minimal association of the mutation with phenotypic drug resistance. There is inconclusive evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 1 but less or equal to 5."}}}}}, "3285": {"$update": {"ARO_description": "A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.", "ARO_category": {"$delete": ["35921", "35999"], "$insert": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}}}}, "3284": {"$update": {"ARO_description": "A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.", "ARO_category": {"$delete": ["35921", "35999"], "$insert": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}}}}, "249": {"$update": {"ARO_category": {"$insert": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}}}}, "1005": {"$update": {"model_param": {"$update": {"40494": {"$update": {"param_description": "A frameshift is a type of genetic mutation caused by a nucleotide insertion or deletion that does not equal 3 bases. This changes the grouping of codons and thus the reading frame during translation, resulting in an incomplete or inactive protein product. Many frameshift mutations generate downstream STOP codons, resulting in premature peptide translation termination. Frameshifts may also confer antibiotic resistance through partial or total protein loss-of-function. Frameshift mutations are included with relevant models when applicable, with the following notation: [wild-type AA][position]fs;[[wild-type AA][position]STOP], where AA is an amino acid. If the premature STOP codon position is unknown or does not exist, [wild-type AA][position]fs is sufficient. Termination can also be denoted as: Ter[position]fs. This parameter is currently not included in detection algorithms."}}}}}}, "1108": {"$update": {"ARO_category": {"$insert": {"36001": {"category_aro_name": "antibiotic efflux", "category_aro_cvterm_id": "36001", "category_aro_accession": "0010000", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Antibiotic resistance via the transport of antibiotics out of the cell."}, "36590": {"category_aro_name": "protein(s) and two-component regulatory system modulating antibiotic efflux", "category_aro_cvterm_id": "36590", "category_aro_accession": "3000451", "category_aro_class_name": "Efflux Regulator", "category_aro_description": "Protein(s) and two component regulatory systems that directly or indirectly change rates of antibiotic efflux."}}}}}, "3649": {"$update": {"model_param": {"$insert": {"43161": {"param_value": {"9876": "-nt-GGATAAAAAGTCTTTTT:A", "9877": "+nt-GGATAAAAAGTCTTTTT:TT"}, "param_type_id": "43161", "param_type": "disruptive mutation in regulatory element", "param_description": "A mutation, i.e. insertion, deletion or other, in the promoter region of a gene which disrupts the translation of that gene, thereby impacting protein function."}}}}}, "1849": {"$update": {"model_param": {"$insert": {"42998": {"param_value": {"9448": "K31fs"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}}}}}, "_timestamp": "2020-05-14T22:13:29+00:00", "1432": {"$update": {"ARO_category": {"$delete": ["39310"], "$insert": {"39140": {"category_aro_name": "ethambutol resistant embC", "category_aro_cvterm_id": "39140", "category_aro_accession": "3002706", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Mycobacterium tuberculosis embC mutations at codon 270 confer resistance to ethambutol."}}}, "model_param": {"$insert": {"43012": {"param_value": {"9490": "V981L", "9491": "N394D", "9493": "T270I"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}, "43010": {"param_value": {"9492": "V987G"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}}}}}, "2270": {"$update": {"ARO_category": {"$update": {"36585": {"$update": {"category_aro_name": "antibiotic-resistant isoleucyl-tRNA synthetase (ileS)"}}}}}}, "3288": {"$update": {"ARO_description": "A tetracycline inactivating enzyme. A flavoenzyme capable of degrading tetracycline antibiotics.", "ARO_category": {"$delete": ["35921", "35999"], "$insert": {"36000": {"category_aro_name": "antibiotic inactivation", "category_aro_cvterm_id": "36000", "category_aro_accession": "0001004", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Enzymatic inactivation of antibiotic to confer drug resistance."}, "36176": {"category_aro_name": "tetracycline inactivation enzyme", "category_aro_cvterm_id": "36176", "category_aro_accession": "3000036", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "Enzymes or other gene products which hydroxylate tetracycline and other tetracycline derivatives. Hydroxylation inactivates tetracycline-like antibiotics, thus conferring resistance to these compounds."}}}}}, "2083": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"9862": "S91I", "9864": "K149R"}, "clinical": {"9862": "S91I", "9864": "K149R"}}}}}}}, "2314": {"$update": {"model_param": {"$update": {"snp": {"$update": {"param_value": {"9882": "S81L", "9881": "G79C"}, "clinical": {"9882": "S81L", "9881": "G79C"}}}}}}}, "1642": {"$update": {"ARO_category": {"$delete": ["36218", "35919"]}}}, "_version": "3.0.9", "2109": {"$update": {"model_param": {"$insert": {"43010": {"param_value": {"9615": "V457L"}, "param_type_id": "43010", "param_type": "Moderate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as moderate confidence has a moderate association of the mutation with phenotypic drug resistance. Additional data is desirable for improved evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 5 but less or equal to 10."}, "43013": {"param_value": {"9632": "I271M"}, "param_type_id": "43013", "param_type": "Indeterminate Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as indeterminate means that there is no statistically significant threshold reached and additional data is required. LR is indeterminate."}, "43012": {"param_value": {"9631": "P94L", "9633": "M291I"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}, "43011": {"param_value": {"9629": "V457L"}, "param_type_id": "43011", "param_type": "Minimal Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as minimal confidence has a minimal association of the mutation with phenotypic drug resistance. There is inconclusive evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 1 but less or equal to 5."}, "42998": {"param_value": {"9616": "E501D", "9630": "N499T"}, "param_type_id": "42998", "param_type": "High Confidence TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as high confidence has a strong association of the mutation with phenotypic drug resistance. There is sufficient evidence that the mutation confers or is strongly associated with drug resistance. LR value is greater than 10."}}}}}, "2144": {"$update": {"ARO_category": {"$delete": ["39310"], "$insert": {"36374": {"category_aro_name": "ethambutol resistant embB", "category_aro_cvterm_id": "36374", "category_aro_accession": "3000235", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "embB gene encodes for an arabinosyl transferase in the arabinogalactan synthesis pathway. It is inhibited by ethambutol. Mutations within the ERDR region of embB confers resistance to ethambutol."}}}}}, "2378": {"$update": {"ARO_category": {"$update": {"41415": {"$update": {"category_aro_name": "antibiotic-resistant cya adenylate cyclase"}}}}}}, "2379": {"$update": {"ARO_category": {"$update": {"41415": {"$update": {"category_aro_name": "antibiotic-resistant cya adenylate cyclase"}}}}}}, "2271": {"$update": {"ARO_category": {"$update": {"36585": {"$update": {"category_aro_name": "antibiotic-resistant isoleucyl-tRNA synthetase (ileS)"}}}}}}, "1943": {"$update": {"model_param": {"$insert": {"43012": {"param_value": {"9551": "G312S"}, "param_type_id": "43012", "param_type": "No association with resistance TB", "param_description": "This parameter is part of a confidence model for AMR developed by the Relational Sequencing Tuberculosis Data platform (ReSeqTB, https://platform.reseqtb.org). The confidence model is based on the likelihood ratio test (LR+) statistic that is used to evaluate whether mutations are positively or negatively associated with phenotypic resistance. The LR+ is derived from a drug susceptibility test, testing sensitivity and specificity. Under the null hypothesis of no association, the LR value is expected to be 1, but deviations from this can be due to an association with resistance or a low number of available isolate samples.  The LR+ measures the strength of association between the presence of a mutation and the drug resistance phenotype. A mutation graded as no association has no association of the mutation with phenotypic drug resistance. There is no evidence of an association between the mutation and drug resistance. LR is less than 1. These data are not visible on the CARD website, included in RGI analyses, nor available in CARD download files."}}}}}, "2290": {"$update": {"ARO_category": {"$update": {"39245": {"$update": {"category_aro_name": "antibiotic-resistant murA transferase"}}}}}}, "2376": {"$update": {"ARO_category": {"$update": {"41412": {"$update": {"category_aro_name": "antibiotic-resistant UhpT"}}}}}}, "2377": {"$update": {"ARO_category": {"$update": {"41414": {"$update": {"category_aro_name": "antibiotic-resistant ptsI phosphotransferase"}}}}}}, "412": {"$update": {"model_sequences": {"$update": {"sequence": {"6040": {"dna_sequence": {"partial": "0", "sequence": "ATGAACATTAAAGCACTCTTACTTATAACAAGCGCTATTTTTATTTCAGCCTGCTCACCTTATATAGTGTCTGCTAATCCAAATCACAGTGCTTCAAAATCTGATGAAAAAGCAGAGAAAATTAAAAATTTATTTAACGAAGCACACACTACGGGTGTTTTAGTTATCCAACAAGGCCAAACTCAACAAAGCTATGGTAATGATCTTGCTCGTGCTTCGACCGAGTATGTACCTGCTTCGACCTTCAAAATGCTTAATGCTTTGATCGGCCTTGAGCACCATAAGGCAACCACTACAGAAGTATTTAAGTGGGACGGGCAAAAAAGGCTATTCCCAGAATGGGAAAAGAACATGACCCTAGGCGATGCTATGAAAGCTTCCGCTATTCCGGTTTATCAAGATTTAGCTCGTCGTATTGGACTTGAACTCATGTCTAATGAAGTGAAGCGTGTTGGTTATGGCAATGCAGATATCGGTACCCAAGTCGATAATTTTTGGCTAGTGGGTCCTTTAAAAATTACTCCTCAGCAAGAGGCACAATTTGCTTACAAGCTAGCTAATAAAACGCTTCCATTTAGCCAAAAAGTCCAAGATGAAGTGCAATCCATGCTATTCATAGAAGAAAAGAATGGAAATAAAATATACGCAAAAAGTGGTTGGGGATGGGATGTAAACCCACAAGTAGGCTGGTTAACTGAATGGGTTGTTCAGCCTCAAGGGAATATTGTAGCGTTCTCCCTTAACTTAGAAATGAAAAAAGGAATACCTAGCTCTGTTCGAAAAGAGATTACTTATAAAAGCTTAGAACAATTAGGTATTTTATAG", "fmax": "825", "accession": "GQ423625.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Acinetobacter baumannii", "NCBI_taxonomy_id": "470", "NCBI_taxonomy_cvterm_id": "35507"}, "protein_sequence": {"accession": "ACV49885.1", "sequence": "MNIKALLLITSAIFISACSPYIVSANPNHSASKSDEKAEKIKNLFNEAHTTGVLVIQQGQTQQSYGNDLARASTEYVPASTFKMLNALIGLEHHKATTTEVFKWDGQKRLFPEWEKNMTLGDAMKASAIPVYQDLARRIGLELMSNEVKRVGYGNADIGTQVDNFWLVGPLKITPQQEAQFAYKLANKTLPFSQKVQDEVQSMLFIEEKNGNKIYAKSGWGWDVNPQVGWLTEWVVQPQGNIVAFSLNLEMKKGIPSSVRKEITYKSLEQLGIL"}}}}}}}, "2372": {"$update": {"ARO_category": {"$update": {"41411": {"$update": {"category_aro_name": "antibiotic-resistant GlpT"}}}}}}, "2373": {"$update": {"ARO_category": {"$update": {"41412": {"$update": {"category_aro_name": "antibiotic-resistant UhpT"}}}}}}}, "$insert": {"3750": {"model_id": "3750", "ARO_accession": "3005006", "model_param": {"blastp_bit_score": {"param_value": "720", "param_type_id": "40725", "param_type": "BLASTP bit-score", "param_description": "A score is a numerical value that describes the overall quality of an alignment with higher numbers correspond to higher similarity. The bit-score (S) is determined by the following formula: S = (\u03bb \u00d7 S \u2212 lnK)/ ln2 where \u03bb is the Gumble distribution constant, S is the raw alignment score, and K is a constant associated with the scoring matrix. Many AMR detection models use this parameter, including the protein homolog and protein variant models. The BLASTP bit-score parameter is a curated value determined from BLASTP analysis of the canonical reference sequence of a specific AMR-associated protein against the database of CARD reference sequence. This value establishes a threshold for computational prediction of a specific protein amongst a batch of submitted sequences."}}, "ARO_description": "A tetracycline efflux MFS Transporter from Providencia sp. Y14", "model_sequences": {"sequence": {"6041": {"dna_sequence": {"partial": "0", "sequence": "ATGAATAAATTTGCGATCACAGCATTAACGATCACCGCCCTTGATGCGATGGGGATCGGGTTGATCATGCCAGTCTTACCAGCCTTACTCCGTGAATATGTCTCCATAGAACACTTGGCAAATCATTACGGCATCTTGTTGGCTTTATATGCCATCATGCAGGTATTTTTTGCCCCGCTACTTGGTAGATGGTCTGATAAATTCGGCCGCAGACCCATCTTGTTGATCTCCCTTGCAGGGGCAGCGCTGGACTACACTTTGTTGGCTTTATCCAGTTCACTATGGATGCTGTATTTAGGCCGCCTAGCCTCAGGGATCACTGGTGCAACAGGTGCGGTAGCCGCTTCTGTTATTGCCGACCATACACAGCCACAACAACGTACCAAGTGGTTTGGTCGTTTAGGGGCTGCGTTTGGCGTGGGTTTAATCGCCGGCCCTGCGATTGGCGGCTTTGCTGGGCAGTTATCTCCTCACTTGCCTTTTGTGATTGCGGCGGTCTTAAATGCATGCTCTTTTGTGGTGATTTGGGTTATTTTTAAAGATCAACGTAAGGCTGTCATACAGGATGCTCAACATGGAGATCAACCGTCGCCAATTCCCTTTATGCAAATAATAAAACCAATCATCCAGCTGCTTTTCGTCTTTTTTATGGCACAGCTCATTGGGCAGATCCCTGCCACTACTTGGGTGTTATTTACCGAAGGCCGCTTTCAGTGGGATAGCATGCAGGTTGGGCTGTCTTTAGCTGGCTTAGGCGTTATGCATGCCCTCTTCCAAGCCTTTGTTGCTGGCGCCATTGCCAAAAAATTCAATGAAAAGGTCACTATCATTGTCGGCTTTGCCCTAGATGGAAGCGCATTTATTATTTTGTCATTACTGGCAGAAGGTTGGTTGATTTACCCTACATTAATCTTACTCGCCGGTGGCAGTATCGCGTTACCCGCATTGCAAAGTTTGATGTCAGCTCAAGTCAACCAAGCTAACCAAGGAAAGCTCCAAGGGGTTTTAGTCAGTTTAACCAATGCCACAGGGGTCATTGGCCCATTATTATTTAGTGTTATTTTTGGCCAAACACTGACGATGTGGGATGGCTGGGTATGGGTGATTGGCGCGATAATGTATGTTTTCTTGATCGTATTTATTTTATCGTTTTATAGAAGCAGCAGACCGACAATTAAACAGCAGACCGACAATTAA", "fmax": "1197", "accession": "KP137702.1", "fmin": "0", "strand": "+"}, "NCBI_taxonomy": {"NCBI_taxonomy_name": "Providencia sp. Y14", "NCBI_taxonomy_id": "1617397", "NCBI_taxonomy_cvterm_id": "42580"}, "protein_sequence": {"accession": "AJO67548.1", "sequence": "MNKFAITALTITALDAMGIGLIMPVLPALLREYVSIEHLANHYGILLALYAIMQVFFAPLLGRWSDKFGRRPILLISLAGAALDYTLLALSSSLWMLYLGRLASGITGATGAVAASVIADHTQPQQRTKWFGRLGAAFGVGLIAGPAIGGFAGQLSPHLPFVIAAVLNACSFVVIWVIFKDQRKAVIQDAQHGDQPSPIPFMQIIKPIIQLLFVFFMAQLIGQIPATTWVLFTEGRFQWDSMQVGLSLAGLGVMHALFQAFVAGAIAKKFNEKVTIIVGFALDGSAFIILSLLAEGWLIYPTLILLAGGSIALPALQSLMSAQVNQANQGKLQGVLVSLTNATGVIGPLLFSVIFGQTLTMWDGWVWVIGAIMYVFLIVFILSFYRSSRPTIKQQTDN"}}}}, "ARO_category": {"36189": {"category_aro_name": "tetracycline antibiotic", "category_aro_cvterm_id": "36189", "category_aro_accession": "3000050", "category_aro_class_name": "Drug Class", "category_aro_description": "These antibiotics are derived from tetracycline, a polyketide antibiotic that inhibits the 30S subunit of bacterial ribosomes."}, "35921": {"category_aro_name": "tetracycline-resistant ribosomal protection protein", "category_aro_cvterm_id": "35921", "category_aro_accession": "0000002", "category_aro_class_name": "AMR Gene Family", "category_aro_description": "A family of proteins known to bind to the 30S ribosomal subunit. This interaction prevents tetracycline and tetracycline derivatives from inhibiting ribosomal function. Thus, these proteins confer elevated resistance to tetracycline derivatives as a ribosomal protection protein."}, "35999": {"category_aro_name": "antibiotic target protection", "category_aro_cvterm_id": "35999", "category_aro_accession": "0001003", "category_aro_class_name": "Resistance Mechanism", "category_aro_description": "Protection of antibiotic action target from antibiotic binding, which process will result in antibiotic resistance."}}, "ARO_name": "tet(57)", "model_type": "protein homolog model", "model_description": "The protein homolog model is an AMR detection model. Protein homolog models detect a protein sequence based on its similarity to a curated reference sequence. A protein homolog model has only one parameter: a curated BLASTP bitscore cutoff for determining the strength of a match. Protein homolog model matches to reference sequences are categorized on three criteria: perfect, strict and loose. A perfect match is 100% identical to the reference sequence along its entire length; a strict match is not identical but the bitscore of the matched sequence is greater than the curated BLASTP bitscore cutoff. Loose matches are other sequences with a match bitscore less than the curated BLASTP bitscore.", "ARO_id": "43194", "model_name": "tet(57)", "model_type_id": "40292"}}}