TB-Profiler result

Run: ERR5917972
Summary

Run ID: ERR5917972

Sample name:

Date: 2024-03-25T21:03:40.053336

Number of reads: 3047166

Percentage reads mapped: 91.49

Median coverage: 97.0

Strain: lineage4.4.1.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.4.1 Euro-American (S-type) None 1.0
lineage4 Euro-American None 1.0
lineage4.4.1.1 Euro-American None 1.0
lineage4.4 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol
pyrazinamide
streptomycin rrs n.799C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rrs 1472644 n.799C>T non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance Mutation from literature
inhA 1673425 c.-777C>T upstream_gene_variant 1.0 isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethionamide Assoc w R Alias fabG1_c.-15C>T
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9138 p.Gln613Glu missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoC 763573 c.204G>C synonymous_variant 0.1 rifampicin Not assoc w R - Interim
rpoC 763578 p.Phe70Tyr missense_variant 0.11 rifampicin
rpoC 763594 c.225C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 764572 c.1203G>C synonymous_variant 0.13 rifampicin
rpoC 764575 c.1206T>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.15 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.11 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>G synonymous_variant 0.12 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777416 c.1065G>T synonymous_variant 1.0 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471923 n.78T>C non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471927 n.82_85delTTCGinsAGCTTGCT non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471932 n.87A>G non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471985 n.140T>C non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1471986 n.141C>T non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472123 n.278A>G non_coding_transcript_exon_variant 0.24 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472151 n.306C>A non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472160 n.315C>T non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472279 n.434T>C non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472285 n.440A>G non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472286 n.441C>G non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472289 n.444T>G non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472290 n.445C>G non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472297 n.453_461delGTCCGGGTT non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472309 n.464C>T non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472311 n.466C>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472312 n.468_470delGAT non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472324 n.479G>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472325 n.480G>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472328 n.483G>C non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
rrs 1472330 n.485G>T non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472344 n.499C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472435 n.590T>C non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472438 n.593T>C non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472439 n.594C>T non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472448 n.603T>C non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472450 n.605A>G non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472451 n.606C>G non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472461 n.616G>C non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472462 n.617T>C non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472464 n.619A>G non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472471 n.626G>A non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472485 n.640delGinsTA non_coding_transcript_exon_variant 0.3 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.3 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472494 n.649A>G non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472498 n.653C>T non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472530 n.685G>A non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472558 n.713G>A non_coding_transcript_exon_variant 0.28 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472569 n.724G>A non_coding_transcript_exon_variant 0.24 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472607 n.762G>A non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472612 n.767G>T non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472660 n.815T>C non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472661 n.816A>G non_coding_transcript_exon_variant 0.2 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472673 n.828T>G non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472674 n.829T>A non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472675 n.832delC non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472714 n.869A>G non_coding_transcript_exon_variant 0.19 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472828 n.983T>C non_coding_transcript_exon_variant 0.12 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472837 n.992C>G non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472838 n.993A>G non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472844 n.999_1000insCG non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472849 n.1005_1006delTA non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472856 n.1011T>C non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrs 1472858 n.1013G>C non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472860 n.1015C>T non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472861 n.1016G>C non_coding_transcript_exon_variant 0.11 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472869 n.1024G>T non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472873 n.1028C>G non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472875 n.1031delG non_coding_transcript_exon_variant 0.11 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472880 n.1035delGinsTCA non_coding_transcript_exon_variant 0.12 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>G non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>C non_coding_transcript_exon_variant 0.36 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473005 n.1160C>T non_coding_transcript_exon_variant 0.4 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.45 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473080 n.1235C>T non_coding_transcript_exon_variant 0.42 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473089 n.1244A>T non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473093 n.1248C>T non_coding_transcript_exon_variant 0.39 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473109 n.1264T>C non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>C non_coding_transcript_exon_variant 0.36 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473115 n.1270G>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.35 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473123 n.1278A>T non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.37 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473148 n.1303G>A non_coding_transcript_exon_variant 0.36 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473163 n.1318C>T non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.32 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473259 n.1414C>T non_coding_transcript_exon_variant 0.34 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.29 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473283 n.1438T>C non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473286 n.1441_1442delCCinsA non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473292 n.1447G>T non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473293 n.1448G>T non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473301 n.1456T>C non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474130 n.473C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474174 n.517A>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474182 n.525C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1474184 n.527C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474185 n.529delA non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474200 n.545delT non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474249 n.592G>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474269 n.612C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474291 n.635_649delTTCCTCTCCGGAGGA non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474351 n.694G>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1474353 n.696A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474356 n.699T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474467 n.810A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1474487 n.830G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474496 n.839C>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474497 n.840G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid Uncertain significance
rrl 1474506 n.849C>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474507 n.850G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474517 n.860C>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474537 n.880G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474749 n.1092C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1096_1097delACinsG non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474774 n.1117A>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474798 n.1141C>A non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474823 n.1166C>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474824 n.1167A>G non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474825 n.1168G>A non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474837 n.1180A>G non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1474864 n.1207C>T non_coding_transcript_exon_variant 0.39 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1474896 n.1239A>G non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474901 n.1244A>G non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1474904 n.1247G>C non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474913 n.1256T>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474921 n.1264C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474932 n.1275C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474951 n.1294C>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474954 n.1297A>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474959 n.1302C>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474963 n.1306G>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1474971 n.1314T>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474974 n.1317G>T non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475458 n.1801C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475478 n.1821_1822delGCinsTGT non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475480 n.1823A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475485 n.1828C>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475486 n.1829A>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475499 n.1842C>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475500 n.1843A>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475531 n.1874C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475538 n.1881T>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475539 n.1882A>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475542 n.1885A>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475544 n.1887A>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475545 n.1888T>G non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475550 n.1893A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475696 n.2039T>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475699 n.2042delCinsGT non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1475703 n.2046A>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475753 n.2096C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475757 n.2100_2101insG non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1475762 n.2105G>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475764 n.2107A>G non_coding_transcript_exon_variant 0.26 capreomycin
linezolid Uncertain significance
rrl 1475765 n.2108A>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1475768 n.2111G>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1475769 n.2112T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1475883 n.2226A>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475884 n.2227A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475897 n.2240T>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475900 n.2243A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1475902 n.2245T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid
rrl 1475916 n.2259C>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.33 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1475997 n.2340A>T non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476030 n.2373A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1476032 n.2375C>G non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1476033 n.2376T>G non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476035 n.2378G>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476044 n.2387T>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1476046 n.2389G>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1476047 n.2390G>T non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476087 n.2430C>T non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476091 n.2434_2435insG non_coding_transcript_exon_variant 0.12 capreomycin
linezolid
rrl 1476099 n.2442A>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476100 n.2443A>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1476105 n.2450delA non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476113 n.2456T>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476164 n.2507A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476194 n.2537A>G non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476200 n.2543A>T non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476201 n.2544C>T non_coding_transcript_exon_variant 0.27 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476245 n.2588C>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476252 n.2595T>G non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476256 n.2599A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.42 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476298 n.2641C>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476300 n.2643G>T non_coding_transcript_exon_variant 0.47 capreomycin
linezolid
rrl 1476301 n.2644A>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476309 n.2652G>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.36 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476524 n.2867_2868delCAinsT non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1476536 n.2879G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476539 n.2882A>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>G non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476572 n.2915G>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid
rpsA 1833829 c.288A>G synonymous_variant 0.1 pyrazinamide
rpsA 1833832 c.291G>A synonymous_variant 0.11 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.11 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.11 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.11 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833862 c.321G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833877 c.336C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833883 c.342C>T synonymous_variant 0.11 pyrazinamide
rpsA 1833884 c.343_345delACCinsGG frameshift_variant&missense_variant 0.11 pyrazinamide Uncertain significance
rpsA 1833894 p.Ala118Glu missense_variant 0.11 pyrazinamide
rpsA 1833914 c.373_375delGCCinsCG frameshift_variant&missense_variant 0.11 pyrazinamide Uncertain significance
rpsA 1833921 p.Lys127Thr missense_variant 0.11 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.13 pyrazinamide
rpsA 1833952 c.411C>T synonymous_variant 0.17 pyrazinamide
rpsA 1833955 c.414G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833970 c.429G>T synonymous_variant 0.16 pyrazinamide
rpsA 1833973 c.432G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.18 pyrazinamide
rpsA 1833997 c.456G>C synonymous_variant 0.22 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834009 c.468C>T synonymous_variant 0.21 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834024 c.483G>C synonymous_variant 0.23 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.21 pyrazinamide
rpsA 1834040 p.Lys167Gln missense_variant 0.21 pyrazinamide
rpsA 1834076 p.Asn179His missense_variant 0.17 pyrazinamide
rpsA 1834093 c.552G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834102 c.561T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834105 c.564C>T synonymous_variant 0.11 pyrazinamide
rpsA 1834108 c.567C>G synonymous_variant 0.11 pyrazinamide
rpsA 1834114 c.573G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834501 c.960G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834519 c.978G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834528 c.987T>G synonymous_variant 0.11 pyrazinamide
rpsA 1834534 c.993C>G synonymous_variant 0.11 pyrazinamide
rpsA 1834537 p.Glu332Asp missense_variant 0.11 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.11 pyrazinamide
rpsA 1834543 c.1002C>G synonymous_variant 0.11 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.11 pyrazinamide
rpsA 1834552 c.1011G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834555 c.1014T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834556 p.Ala339Thr missense_variant 0.12 pyrazinamide Uncertain significance
rpsA 1834565 c.1024_1026delGACinsCG frameshift_variant&missense_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834600 c.1059G>C synonymous_variant 0.12 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.11 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.1 pyrazinamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 1.0 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
whiB7 3568779 c.-100T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 1.0 pyrazinamide Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038836 c.1869G>C synonymous_variant 0.15 pyrazinamide
clpC1 4038842 c.1863G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038845 c.1858_1860delTCGinsAGC synonymous_variant 0.14 pyrazinamide
clpC1 4038860 c.1845G>T synonymous_variant 0.11 pyrazinamide
clpC1 4038863 c.1842G>C synonymous_variant 0.11 pyrazinamide
clpC1 4038872 c.1833C>G synonymous_variant 0.12 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038890 p.Glu605Asp missense_variant 0.14 pyrazinamide
clpC1 4038905 c.1800A>G synonymous_variant 0.12 pyrazinamide
clpC1 4038911 c.1794G>C synonymous_variant 0.12 pyrazinamide
clpC1 4038923 c.1782A>C synonymous_variant 0.11 pyrazinamide
clpC1 4038929 c.1776G>C synonymous_variant 0.1 pyrazinamide
clpC1 4038932 c.1773G>C synonymous_variant 0.1 pyrazinamide
embC 4238963 c.-900C>T upstream_gene_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin