TB-Profiler result

Run: SRR069978
Summary

Run ID: SRR069978

Sample name:

Date: 2024-04-16T13:04:53.417639

Number of reads: 1711216

Percentage reads mapped: 76.54

Median coverage: 27.0

Strain: lineage2.2.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.98
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.94
lineage2.2 East-Asian (Beijing) RD105;RD207 0.83
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG c.1002_1003dupGA Assoc w R High-level resistance
c.496_498delGTTinsAC Assoc w R High-level resistance
kasA p.Asp66Asn Mutation from literature
ethambutol
pyrazinamide
streptomycin rrs n.462C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
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
gyrA 7570 p.Ala90Val missense_variant 0.9 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.27 streptomycin Uncertain significance Mutation from literature
katG 2155108 c.1002_1003dupGA frameshift_variant 0.97 isoniazid Assoc w R High-level resistance
katG 2155614 c.496_498delGTTinsAC frameshift_variant&missense_variant 0.21 isoniazid Assoc w R High-level resistance
kasA 2518310 p.Asp66Asn missense_variant 1.0 isoniazid Mutation from literature
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
dnaA 741 c.741T>C synonymous_variant 0.15 isoniazid Not assoc w R - Interim
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 8156 c.855T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8168 c.867A>G synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 8174 c.873C>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8177 c.876A>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8627 c.1326C>G synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 9200 c.1899A>G synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9204 p.Ser635Thr missense_variant 0.19 levofloxacin
moxifloxacin
gyrA 9227 c.1926C>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9230 c.1929T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 9233 c.1932C>T synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9335 c.2034G>C synonymous_variant 0.15 levofloxacin
moxifloxacin
fgd1 490887 c.105G>C synonymous_variant 0.25 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620784 c.894C>G synonymous_variant 0.21 capreomycin
amikacin
kanamycin
ccsA 620787 c.897C>G synonymous_variant 0.21 capreomycin
amikacin
kanamycin
ccsA 620809 c.919C>T synonymous_variant 0.28 capreomycin
amikacin
kanamycin
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 1.0 ethionamide Uncertain significance
rpoB 760223 c.417T>C synonymous_variant 0.16 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760418 c.612G>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 760424 c.618C>G synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoB 760646 c.840C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760655 c.849A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760670 c.864G>C synonymous_variant 0.13 rifampicin
rpoB 760674 c.868T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760946 c.1140A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760982 c.1176G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761948 c.2142G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761954 c.2148C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761969 c.2163G>A synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761999 c.2193G>C synonymous_variant 0.24 rifampicin
rpoB 762185 c.2379G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762218 c.2412T>G synonymous_variant 0.24 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763040 c.3234C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763076 c.-294C>G upstream_gene_variant 0.26 rifampicin
rpoC 763441 c.72C>G synonymous_variant 0.17 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763468 c.99G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763528 c.159G>A synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.19 rifampicin
rpoC 764040 p.Ser224Asn missense_variant 0.14 rifampicin
rpoC 764044 c.675T>C synonymous_variant 0.16 rifampicin
rpoC 764059 c.690G>C synonymous_variant 0.18 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.21 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.13 rifampicin
rpoC 764257 c.888G>C synonymous_variant 0.21 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.22 rifampicin
rpoC 764269 c.900G>C synonymous_variant 0.26 rifampicin
rpoC 764282 c.913_915delTCGinsAGC synonymous_variant 0.24 rifampicin
rpoC 764405 c.1036A>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.24 rifampicin
rpoC 764716 c.1347G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765352 c.1983G>C synonymous_variant 0.29 rifampicin Not assoc w R - Interim
rpoC 765383 p.Met672Leu missense_variant 0.33 rifampicin Uncertain significance
rpoC 765451 c.2082C>G synonymous_variant 0.22 rifampicin
rpoC 765452 c.2083_2085delGCCinsTG frameshift_variant&missense_variant 0.23 rifampicin
rpoC 765478 c.2109T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 765541 c.2172C>G synonymous_variant 0.29 rifampicin
rpoC 765928 c.2559C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766607 c.3238_3240delATCinsCG frameshift_variant&missense_variant 0.19 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767233 c.3864T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776706 p.Tyr592Phe missense_variant 0.17 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781682 c.123T>C synonymous_variant 0.18 streptomycin
rpsL 781715 c.156T>C synonymous_variant 0.16 streptomycin
rplC 800537 c.-272C>T upstream_gene_variant 0.17 linezolid
rplC 800540 c.-269T>C upstream_gene_variant 0.15 linezolid
rplC 800546 c.-263T>C upstream_gene_variant 0.18 linezolid
rplC 800567 c.-242A>G upstream_gene_variant 0.28 linezolid
rplC 800582 c.-227C>G upstream_gene_variant 0.28 linezolid
rplC 800612 c.-197A>G upstream_gene_variant 0.28 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.26 linezolid
rplC 800654 c.-155T>C upstream_gene_variant 0.19 linezolid
rplC 800865 c.57A>G synonymous_variant 0.21 linezolid
rplC 800867 p.Ser20Asn missense_variant 0.19 linezolid
rplC 800874 c.66A>G synonymous_variant 0.2 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303818 c.888C>G synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1303836 c.906G>C synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fbiC 1303854 c.924T>C synonymous_variant 0.29 clofazimine
pretomanid
delamanid
fbiC 1303860 c.930A>C synonymous_variant 0.29 clofazimine
pretomanid
delamanid
fbiC 1303881 c.951G>C synonymous_variant 0.31 clofazimine
pretomanid
delamanid
fbiC 1303884 c.954T>G synonymous_variant 0.31 clofazimine
pretomanid
delamanid
sigE 1364835 c.423C>G synonymous_variant 0.29 pyrazinamide
sigE 1364839 c.427T>C synonymous_variant 0.3 pyrazinamide
sigE 1364862 c.450C>G synonymous_variant 0.27 pyrazinamide
sigE 1364865 c.453G>C synonymous_variant 0.28 pyrazinamide
sigE 1364866 c.454_456delGCTinsTG frameshift_variant&missense_variant 0.29 pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.2 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473756 n.99G>A non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1473981 n.324delGinsTT non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1473995 n.338G>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.23 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1474104 n.447G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474111 n.454T>C non_coding_transcript_exon_variant 0.3 capreomycin
linezolid
rrl 1474112 n.455T>A non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.34 capreomycin
linezolid
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.3 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.37 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
inhA 1674507 c.306G>C synonymous_variant 0.18 ethionamide
isoniazid
inhA 1674537 c.336C>G synonymous_variant 0.16 ethionamide
isoniazid
inhA 1674624 c.423A>C synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674693 c.492C>G synonymous_variant 0.17 ethionamide
isoniazid
rpsA 1833589 c.48A>T synonymous_variant 0.19 pyrazinamide
rpsA 1833595 c.54T>C synonymous_variant 0.21 pyrazinamide
rpsA 1833619 c.78A>C synonymous_variant 0.3 pyrazinamide
rpsA 1833667 c.126C>G synonymous_variant 0.21 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.27 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.25 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.29 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.39 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.34 pyrazinamide
rpsA 1833790 c.249T>A synonymous_variant 0.35 pyrazinamide
rpsA 1833799 c.258C>G synonymous_variant 0.35 pyrazinamide
rpsA 1833811 c.270G>C synonymous_variant 0.31 pyrazinamide
rpsA 1833838 c.297G>C synonymous_variant 0.24 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.25 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.22 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.39 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.3 pyrazinamide
rpsA 1833970 c.429G>C synonymous_variant 0.36 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.36 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.26 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide Not assoc w R - Interim
rpsA 1834249 c.708T>C synonymous_variant 0.22 pyrazinamide
rpsA 1834297 c.756C>G synonymous_variant 0.27 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.27 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.3 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rpsA 1834375 c.834G>A synonymous_variant 0.21 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834669 c.1128G>C synonymous_variant 0.16 pyrazinamide
ndh 2101939 c.1104A>C synonymous_variant 0.23 ethionamide
delamanid
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2155617 c.495T>C synonymous_variant 0.21 isoniazid Not assoc w R - Interim
katG 2155632 c.480A>C synonymous_variant 0.21 isoniazid
katG 2155637 p.Leu159Ile missense_variant 0.21 isoniazid
katG 2155641 p.Lys157Asn missense_variant 0.22 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser 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
kasA 2517947 c.-168C>T upstream_gene_variant 0.26 isoniazid
kasA 2517974 c.-141T>C upstream_gene_variant 0.19 isoniazid
kasA 2519167 c.1053T>C synonymous_variant 0.33 isoniazid
kasA 2519173 c.1059C>G synonymous_variant 0.33 isoniazid
kasA 2519176 c.1062G>A synonymous_variant 0.33 isoniazid
kasA 2519197 c.1083G>C synonymous_variant 0.23 isoniazid
ahpC 2726638 p.Ala149Val missense_variant 0.2 isoniazid
ahpC 2726645 c.453C>G synonymous_variant 0.21 isoniazid
ahpC 2726657 c.465A>C synonymous_variant 0.19 isoniazid Not assoc w R - Interim
ahpC 2726669 p.Asp159Glu missense_variant 0.16 isoniazid
ahpC 2726672 c.480G>A synonymous_variant 0.17 isoniazid Not assoc w R - Interim
ahpC 2726681 c.489A>G synonymous_variant 0.24 isoniazid
ahpC 2726687 c.495C>G synonymous_variant 0.23 isoniazid
ahpC 2726693 c.501C>G synonymous_variant 0.23 isoniazid
ahpC 2726696 c.504C>G synonymous_variant 0.24 isoniazid
ahpC 2726717 c.525A>G synonymous_variant 0.2 isoniazid
Rv2477c 2782447 c.1596C>T synonymous_variant 0.25 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin
kanamycin
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2782450 c.1593C>G synonymous_variant 0.25 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782453 c.1590C>A synonymous_variant 0.25 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782483 c.1560G>C synonymous_variant 0.29 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783116 c.927T>C synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783485 c.558G>C synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783494 c.549C>G synonymous_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783502 c.541T>C synonymous_variant 0.23 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783953 c.90G>A synonymous_variant 0.38 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783962 c.81T>C synonymous_variant 0.39 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783971 c.72G>C synonymous_variant 0.35 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783980 c.63C>G synonymous_variant 0.31 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783992 c.51T>C synonymous_variant 0.32 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin
Rv2477c 2784428 c.-386T>C upstream_gene_variant 0.23 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784429 c.-387A>G upstream_gene_variant 0.23 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784432 c.-390A>C upstream_gene_variant 0.23 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2752c 3064995 c.1197C>G synonymous_variant 0.18 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
Rv2752c 3064998 c.1194A>G synonymous_variant 0.19 ethambutol
moxifloxacin
levofloxacin
rifampicin
isoniazid
thyX 3067619 c.327A>C synonymous_variant 0.27 para-aminosalicylic_acid
thyX 3067640 c.306G>C synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067643 c.303C>T synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067652 c.294T>C synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067661 c.285C>G synonymous_variant 0.23 para-aminosalicylic_acid
thyX 3067682 c.264G>C synonymous_variant 0.21 para-aminosalicylic_acid
thyX 3067685 c.261A>G synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067688 c.258G>C synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067694 c.252G>C synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067718 c.228C>G synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3073953 c.519T>C synonymous_variant 0.22 para-aminosalicylic_acid
thyA 3073989 c.483T>C synonymous_variant 0.19 para-aminosalicylic_acid
thyA 3074001 c.471C>G synonymous_variant 0.18 para-aminosalicylic_acid
thyA 3074004 c.468T>C synonymous_variant 0.18 para-aminosalicylic_acid
thyA 3074010 c.462C>G synonymous_variant 0.14 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339040 c.-78T>C upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Not assoc w R - Interim
lpqB 3624452 c.459T>G synonymous_variant 0.22 bedaquiline
rifampicin
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625765 c.849C>G synonymous_variant 0.19 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626903 c.-290T>C upstream_gene_variant 0.28 bedaquiline
rifampicin
mtrA 3626912 c.438T>C synonymous_variant 0.29 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626930 c.-317A>T upstream_gene_variant 0.32 bedaquiline
rifampicin
mtrA 3626939 c.411A>G synonymous_variant 0.27 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626942 c.-329A>G upstream_gene_variant 0.29 bedaquiline
rifampicin
mtrA 3627252 p.Ala33Val missense_variant 1.0 bedaquiline
rifampicin
rpoA 3877553 p.Glu319Gln missense_variant 0.36 rifampicin
rpoA 3877818 c.690A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3878725 c.-218A>G upstream_gene_variant 0.29 rifampicin
rpoA 3878737 c.-230G>C upstream_gene_variant 0.23 rifampicin
clpC1 4038790 c.1915C>T synonymous_variant 0.42 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.36 pyrazinamide
clpC1 4038815 c.1890G>T synonymous_variant 0.34 pyrazinamide
clpC1 4038908 c.1797C>G synonymous_variant 0.38 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 0.18 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4039022 c.1683A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039025 c.1680C>T synonymous_variant 0.82 pyrazinamide
clpC1 4039388 c.1317C>A synonymous_variant 0.26 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.26 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.23 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.23 pyrazinamide
clpC1 4039424 c.1281G>A synonymous_variant 0.3 pyrazinamide
clpC1 4039430 c.1275T>C synonymous_variant 0.26 pyrazinamide
clpC1 4039685 c.1020C>T synonymous_variant 0.21 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.26 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.28 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.24 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.27 pyrazinamide
clpC1 4039904 c.801A>G synonymous_variant 0.22 pyrazinamide
clpC1 4040654 c.51G>A synonymous_variant 0.26 pyrazinamide
clpC1 4040657 c.48T>G synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
clpC1 4040662 c.43C>T synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
clpC1 4040699 c.6C>T synonymous_variant 0.17 pyrazinamide
panD 4044188 c.94T>C synonymous_variant 0.19 pyrazinamide
glpK 4138535 c.1221T>C synonymous_variant 0.22 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138538 c.1218C>T synonymous_variant 0.24 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138547 c.1209C>T synonymous_variant 0.24 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4138568 c.1188A>G synonymous_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240780 c.918T>C synonymous_variant 0.17 ethambutol
embC 4240783 c.921G>C synonymous_variant 0.19 ethambutol
embC 4240789 c.927T>C synonymous_variant 0.22 ethambutol
embC 4240867 c.1005T>G synonymous_variant 0.19 ethambutol
embC 4240870 c.1008T>C synonymous_variant 0.18 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4248118 c.1605T>C synonymous_variant 0.3 ethambutol
embB 4248127 c.1614G>C synonymous_variant 0.25 ethambutol
embB 4248133 c.1620C>G synonymous_variant 0.25 ethambutol
embB 4248902 p.Thr797Pro missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269243 p.His197Gln missense_variant 0.19 ethambutol
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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R