TB-Profiler result

Run: SRR28868888
Summary

Run ID: SRR28868888

Sample name:

Date: 2025-02-11T16:36:16.982962

Number of reads: 396251

Percentage reads mapped: 88.21

Median coverage: 13.0

Strain: lineage1.1.3.2

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.1.3 Indo-Oceanic RD239 1.0
lineage1.1.3.2 Indo-Oceanic RD239 0.96
lineage1.1 Indo-Oceanic RD239 1.0
lineage1 Indo-Oceanic RD239 0.92
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol
pyrazinamide
streptomycin gid c.115delC Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
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
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin Assoc w R
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 1393 p.Ala465Thr missense_variant 0.93 isoniazid Uncertain significance
gyrB 5077 c.-163_-162insC upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile 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 7694 c.393A>G synonymous_variant 0.33 levofloxacin
moxifloxacin
gyrA 7697 c.396C>T synonymous_variant 0.32 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7710 c.409T>C synonymous_variant 0.41 levofloxacin
moxifloxacin
gyrA 7715 c.414G>C synonymous_variant 0.4 levofloxacin
moxifloxacin
gyrA 7728 c.427_429delAGGinsCGC synonymous_variant 0.37 levofloxacin
moxifloxacin
gyrA 7742 c.441G>A synonymous_variant 0.42 levofloxacin
moxifloxacin
gyrA 7745 c.444G>A synonymous_variant 0.43 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7758 p.Ile153Val missense_variant 0.5 levofloxacin Uncertain significance
moxifloxacin
gyrA 7763 c.462T>G synonymous_variant 0.48 levofloxacin
moxifloxacin
gyrA 7778 c.477G>T synonymous_variant 0.44 levofloxacin
moxifloxacin
gyrA 7784 c.483A>G synonymous_variant 0.43 levofloxacin
moxifloxacin
gyrA 7787 c.486G>A synonymous_variant 0.44 levofloxacin
moxifloxacin
gyrA 7799 c.498A>G synonymous_variant 0.46 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7835 c.534A>C synonymous_variant 0.38 levofloxacin
moxifloxacin
gyrA 8188 p.Leu296Pro missense_variant 0.94 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8452 p.Ala384Val missense_variant 0.73 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8471 c.1170T>C synonymous_variant 0.41 levofloxacin
moxifloxacin
gyrA 8480 c.1179C>T synonymous_variant 0.41 levofloxacin
moxifloxacin
gyrA 8486 c.1185T>C synonymous_variant 0.4 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8498 c.1197C>T synonymous_variant 0.42 levofloxacin
moxifloxacin
gyrA 8501 c.1200G>C synonymous_variant 0.42 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8504 c.1203G>C synonymous_variant 0.45 levofloxacin
moxifloxacin
gyrA 8513 c.1212C>G synonymous_variant 0.43 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8516 c.1215T>C synonymous_variant 0.43 levofloxacin
moxifloxacin
gyrA 8519 c.1218A>C synonymous_variant 0.43 levofloxacin
moxifloxacin
gyrA 8526 c.1225C>A synonymous_variant 0.47 levofloxacin
moxifloxacin
gyrA 8531 c.1230G>A synonymous_variant 0.43 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8546 c.1245T>C synonymous_variant 0.41 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8552 c.1251C>T synonymous_variant 0.41 levofloxacin
moxifloxacin
gyrA 8555 p.Ala419Gln missense_variant 0.4 levofloxacin
moxifloxacin
gyrA 9143 c.1842T>C synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9227 c.1926C>G synonymous_variant 0.42 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9230 c.1929T>C synonymous_variant 0.42 levofloxacin
moxifloxacin
gyrA 9233 c.1932C>A synonymous_variant 0.43 levofloxacin
moxifloxacin Not assoc w R - Interim
gyrA 9236 c.1935G>C synonymous_variant 0.43 levofloxacin
moxifloxacin
gyrA 9242 c.1941A>C synonymous_variant 0.44 levofloxacin
moxifloxacin
gyrA 9248 c.1947G>C synonymous_variant 0.44 levofloxacin
moxifloxacin
gyrA 9252 p.Val651Ile missense_variant 0.44 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9257 c.1956C>T synonymous_variant 0.46 levofloxacin
moxifloxacin
gyrA 9267 p.Asn656Gly missense_variant 0.47 levofloxacin
moxifloxacin
gyrA 9281 c.1980C>G synonymous_variant 0.49 levofloxacin
moxifloxacin
gyrA 9284 c.1983T>A synonymous_variant 0.49 levofloxacin
moxifloxacin
gyrA 9296 c.1995T>C synonymous_variant 0.57 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9299 c.1998G>C synonymous_variant 0.55 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Glu missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9323 c.2022C>G synonymous_variant 0.65 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9335 c.2034G>C synonymous_variant 0.6 levofloxacin
moxifloxacin
gyrA 9356 c.2055G>C synonymous_variant 0.58 levofloxacin
moxifloxacin
gyrA 9362 c.2061C>T synonymous_variant 0.54 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9377 c.2076A>G synonymous_variant 0.43 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9383 c.2082T>C synonymous_variant 0.36 levofloxacin
moxifloxacin
gyrA 9386 c.2085T>C synonymous_variant 0.35 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9395 c.2094G>T synonymous_variant 0.32 levofloxacin
moxifloxacin
gyrA 9413 c.2112G>A synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 9419 c.2118T>C synonymous_variant 0.29 levofloxacin
moxifloxacin
gyrA 9420 p.Ile707Ala missense_variant 0.29 levofloxacin
moxifloxacin
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
ccsA 620592 c.702C>T synonymous_variant 0.38 kanamycin
capreomycin
amikacin
ccsA 620604 c.714C>G synonymous_variant 0.36 kanamycin
capreomycin
amikacin
ccsA 620607 c.717T>G synonymous_variant 0.36 kanamycin
capreomycin
amikacin
ccsA 620625 c.735A>C synonymous_variant 0.38 kanamycin
capreomycin
amikacin
ccsA 620631 c.741T>G synonymous_variant 0.38 kanamycin
capreomycin
amikacin
ccsA 620634 c.744C>G synonymous_variant 0.38 kanamycin
capreomycin
amikacin
ccsA 620648 p.Glu253Gly missense_variant 0.4 kanamycin
capreomycin
amikacin
ccsA 620652 c.762C>G synonymous_variant 0.38 kanamycin
capreomycin
amikacin
ccsA 620694 c.804C>G synonymous_variant 0.29 kanamycin
capreomycin
amikacin
ccsA 620698 p.Val270Ile missense_variant 0.29 kanamycin
capreomycin
amikacin
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
rpoB 761240 c.1434C>T synonymous_variant 0.35 rifampicin
rpoB 761249 c.1443A>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 761258 c.1452G>A synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoB 761282 c.1476C>A synonymous_variant 0.58 rifampicin
rpoB 761318 c.1512G>T synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoB 761327 c.1521A>G synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoB 761330 c.1524G>C synonymous_variant 0.58 rifampicin
rpoB 761333 c.1527G>C synonymous_variant 0.56 rifampicin
rpoB 761345 c.1539G>C synonymous_variant 0.5 rifampicin
rpoB 761346 p.Val514Asn missense_variant 0.5 rifampicin
rpoB 761354 c.1548C>T synonymous_variant 0.48 rifampicin
rpoB 761360 c.1554T>C synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoB 761369 p.Glu521Asp missense_variant 0.36 rifampicin
rpoB 761374 p.Val523Glu missense_variant 0.35 rifampicin
rpoB 761408 c.1602G>C synonymous_variant 0.29 rifampicin
rpoB 761561 c.1755C>G synonymous_variant 0.55 rifampicin
rpoB 761564 c.1758G>C synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.58 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.59 rifampicin
rpoB 761657 c.1851C>G synonymous_variant 0.6 rifampicin Not assoc w R - Interim
rpoB 761669 c.1863C>T synonymous_variant 0.63 rifampicin
rpoB 761675 c.1869G>C synonymous_variant 0.66 rifampicin
rpoB 761690 c.1884G>C synonymous_variant 0.62 rifampicin
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 1.0 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 765230 p.Ala621Thr missense_variant 1.0 rifampicin Not assoc w R
rpoC 765526 c.2157C>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 765533 p.Tyr722His missense_variant 0.48 rifampicin Uncertain significance
rpoC 765547 c.2178C>T synonymous_variant 0.56 rifampicin Not assoc w R - Interim
rpoC 765548 c.2179_2181delAGCinsTCG synonymous_variant 0.56 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.59 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.63 rifampicin
rpoC 765562 c.2193G>C synonymous_variant 0.61 rifampicin
rpoC 765611 p.His748Ser missense_variant 0.57 rifampicin Uncertain significance
rpoC 765625 c.2256C>T synonymous_variant 0.55 rifampicin
rpoC 765628 c.2259G>C synonymous_variant 0.55 rifampicin Not assoc w R - Interim
rpoC 765635 p.Val756Leu missense_variant 0.57 rifampicin
rpoC 765640 c.2271A>G synonymous_variant 0.56 rifampicin
rpoC 765658 c.2289C>T synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoC 765661 c.2292T>C synonymous_variant 0.39 rifampicin
rpoC 765662 c.2293_2295delTTGinsCTC synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 765669 p.His767Arg missense_variant 0.43 rifampicin
rpoC 765673 p.Asp768Glu missense_variant 0.43 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 765835 c.2466C>T synonymous_variant 0.45 rifampicin Not assoc w R - Interim
rpoC 765859 c.2490G>A synonymous_variant 0.54 rifampicin Not assoc w R - Interim
rpoC 765871 c.2502T>C synonymous_variant 0.65 rifampicin
rpoC 765875 p.Val836Ile missense_variant 0.68 rifampicin Uncertain significance
rpoC 765904 c.2535C>G synonymous_variant 0.71 rifampicin Not assoc w R - Interim
rpoC 765934 c.2565C>T synonymous_variant 0.79 rifampicin
rpoC 765967 c.2598C>T synonymous_variant 0.77 rifampicin Not assoc w R - Interim
rpoC 765973 c.2604C>T synonymous_variant 0.77 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.76 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>T synonymous_variant 0.74 rifampicin Not assoc w R - Interim
rpoC 765991 c.2622C>G synonymous_variant 0.75 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.75 rifampicin Not assoc w R - Interim
rpoC 766000 c.2631G>C synonymous_variant 0.76 rifampicin
rpoC 766003 c.2634G>C synonymous_variant 0.73 rifampicin
rpoC 766009 c.2640G>C synonymous_variant 0.72 rifampicin Not assoc w R - Interim
rpoC 766043 p.Gln892Gly missense_variant 0.64 rifampicin
rpoC 766069 p.Glu900Asp missense_variant 0.35 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 801166 p.Gly120Ser missense_variant 1.0 linezolid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>T non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>T non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475209 n.1552G>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid
rrl 1475221 n.1564C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid Uncertain significance
inhA 1674534 c.333G>C synonymous_variant 0.6 isoniazid Not assoc w R - Interim
ethionamide
inhA 1674539 p.Tyr113Phe missense_variant 0.62 isoniazid
ethionamide
inhA 1674542 p.Ala114Glu missense_variant 0.62 isoniazid
ethionamide
inhA 1674546 c.345T>C synonymous_variant 0.61 isoniazid
ethionamide
inhA 1674550 p.Ser117Ala missense_variant 0.56 isoniazid
ethionamide
inhA 1674573 c.372G>C synonymous_variant 0.63 isoniazid
ethionamide
inhA 1674576 c.375T>C synonymous_variant 0.62 isoniazid
ethionamide
inhA 1674579 c.378G>C synonymous_variant 0.67 isoniazid
ethionamide
inhA 1674585 c.384T>C synonymous_variant 0.63 isoniazid
ethionamide
inhA 1674589 p.Met130Leu missense_variant 0.63 isoniazid
ethionamide
inhA 1674597 c.396G>A synonymous_variant 0.59 isoniazid
ethionamide
inhA 1674600 c.399G>C synonymous_variant 0.62 isoniazid
ethionamide
inhA 1674618 c.417C>T synonymous_variant 0.61 isoniazid
ethionamide
inhA 1674624 c.423A>C synonymous_variant 0.65 isoniazid
ethionamide
inhA 1674627 c.426T>C synonymous_variant 0.65 isoniazid
ethionamide
inhA 1674628 p.Ser143Gly missense_variant 0.67 isoniazid
ethionamide
inhA 1674654 c.453G>C synonymous_variant 0.67 isoniazid
ethionamide
inhA 1674656 p.Ser152Thr missense_variant 0.68 isoniazid
ethionamide
inhA 1674690 c.489C>G synonymous_variant 0.68 isoniazid
ethionamide
inhA 1674702 c.501G>A synonymous_variant 0.67 isoniazid
ethionamide
inhA 1674703 c.502T>C synonymous_variant 0.67 isoniazid
ethionamide
inhA 1674714 c.513C>G synonymous_variant 0.64 isoniazid
ethionamide
inhA 1674718 c.517A>C synonymous_variant 0.62 isoniazid
ethionamide
rpsA 1834451 c.910T>C synonymous_variant 0.48 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.42 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.42 pyrazinamide
rpsA 1834477 c.936C>T synonymous_variant 0.42 pyrazinamide Not assoc w R - Interim
rpsA 1834489 c.948T>C synonymous_variant 0.41 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.4 pyrazinamide
rpsA 1834522 c.981C>T synonymous_variant 0.47 pyrazinamide
rpsA 1834527 p.Arg329His missense_variant 0.47 pyrazinamide
rpsA 1834540 c.999G>T synonymous_variant 0.47 pyrazinamide Not assoc w R - Interim
rpsA 1834543 c.1002C>G synonymous_variant 0.53 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.5 pyrazinamide
rpsA 1834552 c.1011G>T synonymous_variant 0.42 pyrazinamide
rpsA 1834555 c.1014T>C synonymous_variant 0.45 pyrazinamide
rpsA 1834558 c.1017C>G synonymous_variant 0.53 pyrazinamide
rpsA 1834573 c.1032G>C synonymous_variant 0.4 pyrazinamide
rpsA 1834603 p.Glu354Asp missense_variant 0.38 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.38 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.38 pyrazinamide
rpsA 1834690 c.1149T>C synonymous_variant 0.55 pyrazinamide
rpsA 1834732 c.1191T>C synonymous_variant 0.67 pyrazinamide
rpsA 1834738 c.1197A>G synonymous_variant 0.64 pyrazinamide
rpsA 1834747 c.1206A>G synonymous_variant 0.63 pyrazinamide
rpsA 1834751 p.Leu404Ile missense_variant 0.63 pyrazinamide
rpsA 1834756 c.1215G>A synonymous_variant 0.63 pyrazinamide
rpsA 1834759 c.1218A>T synonymous_variant 0.63 pyrazinamide
rpsA 1834765 p.Glu408Asp missense_variant 0.61 pyrazinamide
rpsA 1834775 p.Ala412Thr missense_variant 0.61 pyrazinamide
rpsA 1834780 c.1239A>G synonymous_variant 0.63 pyrazinamide
rpsA 1834786 c.1245A>G synonymous_variant 0.67 pyrazinamide
rpsA 1834789 c.1248T>C synonymous_variant 0.67 pyrazinamide
rpsA 1834792 c.1251G>C synonymous_variant 0.67 pyrazinamide
rpsA 1834804 c.1263C>T synonymous_variant 0.69 pyrazinamide
tsnR 1853361 c.-245T>C upstream_gene_variant 0.67 linezolid
tsnR 1853370 c.-236_-234delGCAinsTCC upstream_gene_variant 0.72 linezolid
tsnR 1853375 c.-231G>C upstream_gene_variant 0.68 linezolid
tsnR 1853387 c.-219T>G upstream_gene_variant 0.72 linezolid
tsnR 1853390 c.-216G>C upstream_gene_variant 0.72 linezolid
tsnR 1853394 c.-212_-211delCTinsGC upstream_gene_variant 0.74 linezolid
tsnR 1853420 c.-186T>G upstream_gene_variant 0.71 linezolid
tsnR 1853429 c.-177G>C upstream_gene_variant 0.66 linezolid
tsnR 1853432 c.-174G>C upstream_gene_variant 0.62 linezolid
tsnR 1853444 c.-162C>T upstream_gene_variant 0.58 linezolid
tsnR 1853453 c.-153G>C upstream_gene_variant 0.5 linezolid
tsnR 1853974 c.369C>T synonymous_variant 1.0 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
kasA 2517917 c.-198G>T upstream_gene_variant 0.47 isoniazid
kasA 2517926 c.-189G>A upstream_gene_variant 0.44 isoniazid
kasA 2517941 c.-174C>G upstream_gene_variant 0.39 isoniazid
kasA 2517950 c.-165C>G upstream_gene_variant 0.37 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
ahpC 2726271 p.Asp27Asn missense_variant 1.0 isoniazid
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625678 c.-768C>G upstream_gene_variant 0.45 rifampicin
bedaquiline
lpqB 3625683 c.-773C>T upstream_gene_variant 0.48 rifampicin
bedaquiline
lpqB 3625687 c.-777G>T upstream_gene_variant 0.48 rifampicin
bedaquiline
lpqB 3625690 c.-780T>C upstream_gene_variant 0.48 rifampicin
bedaquiline
lpqB 3625720 c.-810G>A upstream_gene_variant 0.52 rifampicin
bedaquiline
lpqB 3625723 c.-813C>G upstream_gene_variant 0.54 rifampicin
bedaquiline
mtrB 3625729 c.885A>G synonymous_variant 0.54 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625747 c.867G>C synonymous_variant 0.61 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625755 p.Ala287Thr missense_variant 0.62 rifampicin Uncertain significance
bedaquiline
mtrB 3625762 c.852A>T synonymous_variant 0.59 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625765 c.849C>G synonymous_variant 0.59 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625768 c.-858G>C upstream_gene_variant 0.59 rifampicin
bedaquiline
mtrB 3625774 c.840G>A synonymous_variant 0.64 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625806 c.808A>C synonymous_variant 0.61 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625819 c.795G>A synonymous_variant 0.54 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625822 c.-912C>T upstream_gene_variant 0.51 rifampicin
bedaquiline
mtrB 3625837 c.777C>G synonymous_variant 0.53 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625852 c.-942A>C upstream_gene_variant 0.45 rifampicin
bedaquiline
lpqB 3625864 c.-954T>A upstream_gene_variant 0.45 rifampicin
bedaquiline
mtrB 3625867 c.747A>G synonymous_variant 0.45 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3625879 c.-969G>C upstream_gene_variant 0.41 rifampicin
bedaquiline
lpqB 3625882 c.-972G>T upstream_gene_variant 0.38 rifampicin
bedaquiline
lpqB 3625885 c.-975G>A upstream_gene_variant 0.32 rifampicin
bedaquiline
lpqB 3625888 c.-978G>C upstream_gene_variant 0.32 rifampicin
bedaquiline
ddn 3986749 c.-95C>A upstream_gene_variant 1.0 pretomanid
delamanid
clpC1 4040135 c.570C>G synonymous_variant 0.41 pyrazinamide
clpC1 4040144 c.561G>C synonymous_variant 0.41 pyrazinamide
clpC1 4040147 c.558A>G synonymous_variant 0.41 pyrazinamide Not assoc w R - Interim
clpC1 4040153 c.552A>G synonymous_variant 0.46 pyrazinamide
clpC1 4040159 c.546G>C synonymous_variant 0.48 pyrazinamide
clpC1 4040162 c.543G>C synonymous_variant 0.48 pyrazinamide Not assoc w R - Interim
clpC1 4040168 c.537G>C synonymous_variant 0.44 pyrazinamide
clpC1 4040171 c.534C>G synonymous_variant 0.44 pyrazinamide
clpC1 4040180 c.525C>G synonymous_variant 0.52 pyrazinamide
clpC1 4040201 c.504C>G synonymous_variant 0.52 pyrazinamide
clpC1 4040204 c.501G>C synonymous_variant 0.47 pyrazinamide
clpC1 4040237 c.468C>G synonymous_variant 0.5 pyrazinamide
clpC1 4040480 c.225T>C synonymous_variant 0.46 pyrazinamide Not assoc w R - Interim
clpC1 4040501 c.204C>A synonymous_variant 0.56 pyrazinamide
clpC1 4040513 c.192G>A synonymous_variant 0.58 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.44 pyrazinamide Not assoc w R - Interim
clpC1 4040522 c.183T>C synonymous_variant 0.56 pyrazinamide Not assoc w R - Interim
clpC1 4040531 c.174T>C synonymous_variant 0.61 pyrazinamide
clpC1 4040546 c.159G>T synonymous_variant 0.58 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4138565 c.1191G>C synonymous_variant 0.39 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138568 c.1188A>C synonymous_variant 0.4 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138571 c.1185C>G synonymous_variant 0.41 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138574 c.1182G>C synonymous_variant 0.44 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138580 c.1176C>T synonymous_variant 0.41 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138598 c.1158G>C synonymous_variant 0.34 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138601 c.1155G>C synonymous_variant 0.36 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138604 c.1150_1152delTTGinsCTT synonymous_variant 0.36 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138631 c.1125C>G synonymous_variant 0.34 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138634 c.1122G>T synonymous_variant 0.37 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138643 c.1113A>G synonymous_variant 0.35 levofloxacin
moxifloxacin
isoniazid Not assoc w R - Interim
streptomycin
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
glpK 4138654 c.1102C>T synonymous_variant 0.38 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
glpK 4138655 c.1101G>C synonymous_variant 0.36 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138661 c.1095T>C synonymous_variant 0.38 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138676 c.1080T>C synonymous_variant 0.39 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138682 c.1074C>G synonymous_variant 0.32 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
glpK 4138696 p.Pro354Ser missense_variant 0.26 levofloxacin
moxifloxacin
isoniazid Uncertain significance
streptomycin
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.84 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Not assoc w R
embA 4244853 p.Val541Ile missense_variant 0.35 ethambutol
embA 4244856 p.Ala542Asn missense_variant 0.33 ethambutol
embA 4244862 p.Leu544Val missense_variant 0.32 ethambutol
embA 4244885 c.1653A>G synonymous_variant 0.35 ethambutol
embA 4244894 c.1662C>G synonymous_variant 0.35 ethambutol
embA 4244895 p.Thr555Ser missense_variant 0.35 ethambutol
embA 4244900 c.1668G>C synonymous_variant 0.35 ethambutol
embA 4244906 c.1674C>G synonymous_variant 0.35 ethambutol
embA 4244921 c.1689C>G synonymous_variant 0.38 ethambutol
embA 4244924 c.1692G>C synonymous_variant 0.38 ethambutol Not assoc w R - Interim
embA 4244930 c.1698G>C synonymous_variant 0.38 ethambutol
embA 4244933 c.1701A>G synonymous_variant 0.37 ethambutol
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 1.0 streptomycin Not assoc w R