TB-Profiler result

Run: SRR1181251
Summary

Run ID: SRR1181251

Sample name:

Date: 2024-04-15T14:41:46.861450

Number of reads: 3510673

Percentage reads mapped: 79.04

Median coverage: 79.5

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.99
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.98
lineage2.2 East-Asian (Beijing) RD105;RD207 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid
ethambutol embB p.His312Arg Mutation from literature
pyrazinamide
streptomycin
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
embB 4247448 p.His312Arg missense_variant 0.14 ethambutol 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
gyrB 6307 c.1068T>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6730 c.-572A>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7541 c.240C>G synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7547 c.246C>T synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7595 c.294C>G synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 7601 c.300C>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7799 c.498A>G synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8603 c.1302A>G synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8609 c.1308G>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8619 c.1318T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8645 c.1344C>T synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491106 c.324T>C synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 0.99 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.9 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620415 c.525T>C synonymous_variant 0.15 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
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
nusG 734532 c.279A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760235 c.429T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760611 c.805T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761561 c.1755C>G synonymous_variant 0.15 rifampicin
rpoB 761564 c.1758G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.15 rifampicin
rpoB 761612 c.1806G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762114 p.Ile770Val missense_variant 0.17 rifampicin Uncertain significance
rpoB 762185 c.2379G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762254 c.2448T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 762395 c.-975G>C upstream_gene_variant 0.15 rifampicin
rpoB 762404 c.2598T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 762410 c.-960T>C upstream_gene_variant 0.17 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762470 c.2664G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762857 c.3051C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763028 c.3222T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763127 c.3321G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763169 c.-201A>G upstream_gene_variant 0.22 rifampicin
rpoC 763202 c.-168A>G upstream_gene_variant 0.16 rifampicin
rpoC 763206 c.-164_-163delAGinsTC upstream_gene_variant 0.15 rifampicin
rpoC 763486 c.117T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763714 c.345G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763732 c.363C>G synonymous_variant 0.21 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.19 rifampicin
rpoC 763781 p.Ser138Ala missense_variant 0.18 rifampicin
rpoC 764024 c.655T>C synonymous_variant 0.14 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.22 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764278 c.909A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764284 c.915G>C synonymous_variant 0.17 rifampicin
rpoC 764317 c.948C>G synonymous_variant 0.2 rifampicin
rpoC 764320 c.951C>T synonymous_variant 0.16 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764387 c.1018T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.16 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 0.17 rifampicin Not assoc w R - Interim
rpoC 764668 c.1299C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764746 c.1377G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764923 c.1554A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>G synonymous_variant 0.14 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765547 c.2178C>A synonymous_variant 0.16 rifampicin
rpoC 765556 c.2187G>C synonymous_variant 0.18 rifampicin
rpoC 765562 c.2193G>C synonymous_variant 0.18 rifampicin
rpoC 765583 c.2214G>T synonymous_variant 0.17 rifampicin
rpoC 765628 c.2259G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765700 c.2331T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765835 c.2466C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765883 c.2514C>G synonymous_variant 0.15 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.16 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765994 c.2625A>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766408 c.3039C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 766426 c.3057C>T synonymous_variant 0.21 rifampicin
rpoC 766486 c.3117A>G synonymous_variant 0.17 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.21 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.21 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.23 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 767002 c.3633G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.27 rifampicin
rpoC 767044 c.3675G>A synonymous_variant 0.14 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.26 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767221 c.3852C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767233 c.3864T>C synonymous_variant 0.15 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 776182 p.Asp767Asn missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.98 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 0.98 streptomycin Not assoc w R
rpsL 781649 c.90T>C synonymous_variant 0.14 streptomycin
rpsL 781655 c.96T>C synonymous_variant 0.15 streptomycin
rpsL 781709 c.150G>C synonymous_variant 0.14 streptomycin Not assoc w R - Interim
rpsL 781715 c.156T>C synonymous_variant 0.15 streptomycin
rpsL 781718 c.159C>G synonymous_variant 0.15 streptomycin
rpsL 781721 c.162C>G synonymous_variant 0.14 streptomycin
rpsL 781728 c.169T>C synonymous_variant 0.2 streptomycin
rpsL 781760 c.201T>C synonymous_variant 0.25 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.16 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.14 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.13 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.15 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.14 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.16 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.15 streptomycin Uncertain significance
rplC 800579 c.-230C>T upstream_gene_variant 0.15 linezolid
rplC 800582 c.-227C>G upstream_gene_variant 0.15 linezolid
rplC 800612 c.-197A>G upstream_gene_variant 0.19 linezolid
rplC 800618 c.-191T>C upstream_gene_variant 0.2 linezolid
rplC 800648 c.-161A>C upstream_gene_variant 0.19 linezolid
rplC 800693 c.-116A>C upstream_gene_variant 0.19 linezolid
rplC 800759 c.-50C>T upstream_gene_variant 0.13 linezolid
rplC 800865 c.57A>G synonymous_variant 0.14 linezolid
rplC 800922 c.114C>G synonymous_variant 0.14 linezolid
rplC 801210 c.402T>C synonymous_variant 0.16 linezolid
rplC 801312 c.504G>C synonymous_variant 0.17 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 1303545 c.615A>G synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1304832 c.1902C>T synonymous_variant 0.15 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 1.0 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
atpE 1461219 c.175T>C synonymous_variant 0.15 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471935 n.90T>C non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471970 n.125G>A non_coding_transcript_exon_variant 0.13 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472075 n.230A>G non_coding_transcript_exon_variant 0.13 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.14 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.21 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473877 n.220G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1473887 n.230T>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1473888 n.231T>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474034 n.377G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474083 n.426C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1474103 n.446A>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474632 n.975G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474673 n.1016T>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474717 n.1060A>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476035 n.2378G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476086 n.2429G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rpsA 1833727 c.186G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
tsnR 1853574 c.-32T>C upstream_gene_variant 1.0 linezolid
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
bacA 2064240 c.487_489delCAAinsAG frameshift_variant&synonymous_variant 0.15 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
bacA 2064243 c.486A>C synonymous_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
bacA 2064269 c.460A>C synonymous_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
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 2517941 c.-174C>G upstream_gene_variant 0.17 isoniazid
kasA 2518642 c.528A>G synonymous_variant 0.16 isoniazid
kasA 2518648 c.534C>T synonymous_variant 0.13 isoniazid
kasA 2518672 c.558G>C synonymous_variant 0.22 isoniazid
kasA 2518681 c.567C>T synonymous_variant 0.16 isoniazid
kasA 2518684 c.570C>A synonymous_variant 0.16 isoniazid
kasA 2518711 c.597A>G synonymous_variant 0.22 isoniazid
kasA 2518747 c.633C>G synonymous_variant 0.18 isoniazid
kasA 2518864 c.750G>C synonymous_variant 0.14 isoniazid
kasA 2518885 c.771T>C synonymous_variant 0.18 isoniazid
kasA 2518939 c.825T>C synonymous_variant 0.15 isoniazid
kasA 2518942 c.828T>C synonymous_variant 0.16 isoniazid
kasA 2518951 c.837G>A synonymous_variant 0.16 isoniazid
Rv2477c 2783158 c.885A>C synonymous_variant 0.14 ethambutol Not assoc w R - Interim
moxifloxacin
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 2783194 c.849A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783359 c.684G>A synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783395 c.648T>C synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783410 c.633G>C synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783422 c.621T>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783428 c.615C>T synonymous_variant 0.16 ethambutol
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 2783674 c.369T>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783700 p.Thr115Ser missense_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783860 c.183T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783883 c.160T>C synonymous_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783884 c.159T>A synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783956 c.87T>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783971 c.72G>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783992 c.51T>C synonymous_variant 0.13 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 2784454 c.-412G>A upstream_gene_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784477 c.-435T>C upstream_gene_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2784492 c.-450C>G upstream_gene_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
thyX 3067316 c.630A>G synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067325 c.621A>G synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067373 c.573C>G synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067874 c.72C>G synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3073932 c.540C>T synonymous_variant 0.18 para-aminosalicylic_acid
thyA 3073989 c.483T>C synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3074004 c.468T>C synonymous_variant 0.13 para-aminosalicylic_acid
thyA 3074031 c.441T>C synonymous_variant 0.15 para-aminosalicylic_acid
thyA 3074037 c.435C>G synonymous_variant 0.14 para-aminosalicylic_acid
thyA 3074053 p.Arg140Gln missense_variant 0.15 para-aminosalicylic_acid
thyA 3074056 p.Glu139Pro missense_variant 0.15 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.97 pyrazinamide Not assoc w R - Interim
lpqB 3624071 c.840C>T synonymous_variant 0.17 bedaquiline
rifampicin
lpqB 3624080 c.831G>A synonymous_variant 0.17 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3624107 c.804C>T synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627056 c.294C>T synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627071 c.-458G>C upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrA 3627080 c.270T>C synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627083 c.-470G>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrA 3627098 c.252A>C synonymous_variant 0.2 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627104 c.-491C>G upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrB 3627272 c.-659G>T upstream_gene_variant 0.14 bedaquiline
rifampicin
fbiA 3640298 c.-245A>G upstream_gene_variant 0.13 clofazimine
pretomanid
delamanid
rpoA 3877668 c.840A>G synonymous_variant 0.19 rifampicin
rpoA 3877680 c.828G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878157 c.351C>G synonymous_variant 0.18 rifampicin
rpoA 3878163 c.345C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878193 c.315T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3878247 c.261G>C synonymous_variant 0.26 rifampicin
rpoA 3878256 c.252G>C synonymous_variant 0.28 rifampicin
rpoA 3878262 c.246C>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoA 3878271 c.237T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoA 3878283 p.Glu75Asp missense_variant 0.24 rifampicin Uncertain significance
rpoA 3878295 c.213A>G synonymous_variant 0.18 rifampicin
rpoA 3878298 c.210A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878334 c.174T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3878809 c.-302T>C upstream_gene_variant 0.18 rifampicin
rpoA 3878853 c.-346G>A upstream_gene_variant 0.23 rifampicin
rpoA 3878878 c.-371T>C upstream_gene_variant 0.21 rifampicin Uncertain significance
rpoA 3879088 c.-581A>C upstream_gene_variant 0.19 rifampicin
rpoA 3879094 c.-587T>C upstream_gene_variant 0.21 rifampicin
rpoA 3879121 c.-614T>G upstream_gene_variant 0.25 rifampicin
rpoA 3879154 c.-647T>C upstream_gene_variant 0.19 rifampicin
rpoA 3879160 c.-653A>G upstream_gene_variant 0.2 rifampicin
clpC1 4038519 p.Arg729Gln missense_variant 0.2 pyrazinamide
clpC1 4038530 p.Glu725Asp missense_variant 0.21 pyrazinamide
clpC1 4038536 c.2169C>T synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
clpC1 4038596 c.2109A>G synonymous_variant 0.14 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 0.15 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039085 c.1620A>G synonymous_variant 0.17 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039103 c.1602T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039574 c.1131G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039589 c.1116G>T synonymous_variant 0.14 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.19 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.18 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039751 c.954A>G synonymous_variant 0.15 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.13 pyrazinamide
clpC1 4040444 c.261C>T synonymous_variant 0.17 pyrazinamide
clpC1 4040459 c.246C>G synonymous_variant 0.18 pyrazinamide
clpC1 4040471 c.234T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4040480 c.225T>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
clpC1 4040522 c.183T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4040528 c.177G>C synonymous_variant 0.13 pyrazinamide
embC 4240486 c.624G>A synonymous_variant 0.16 ethambutol
embC 4240489 c.627A>G synonymous_variant 0.16 ethambutol
embC 4240495 c.633T>C synonymous_variant 0.17 ethambutol
embC 4241140 c.1278A>G synonymous_variant 0.15 ethambutol Not assoc w R - Interim
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 4246567 c.54G>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embB 4247470 c.957T>C synonymous_variant 0.17 ethambutol
embB 4247497 c.984T>C synonymous_variant 0.16 ethambutol
embB 4247500 c.987C>G synonymous_variant 0.16 ethambutol
embB 4247512 c.999T>C synonymous_variant 0.17 ethambutol
embB 4247590 c.1077A>G synonymous_variant 0.16 ethambutol Not assoc w R - Interim
embB 4248070 c.1557T>C synonymous_variant 0.13 ethambutol
embB 4248277 c.1764G>C synonymous_variant 0.15 ethambutol
aftB 4267535 c.1302A>G synonymous_variant 0.13 ethambutol
aftB 4267556 c.1281G>C synonymous_variant 0.14 ethambutol
aftB 4267622 c.1213_1215delTCGinsAC frameshift_variant&missense_variant 0.14 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.87 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
gid 4407588 c.615A>G synonymous_variant 0.99 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R