TB-Profiler result

Run: ERR400529
Summary

Run ID: ERR400529

Sample name:

Date: 2024-04-15T09:12:48.222376

Number of reads: 2644039

Percentage reads mapped: 82.81

Median coverage: 56.0

Strain: lineage3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 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
pyrazinamide
streptomycin rrs n.190G>A Mutation from literature
n.462C>T Uncertain significance Mutation from literature
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
rrs 1472035 n.190G>A non_coding_transcript_exon_variant 0.14 streptomycin Mutation from literature
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.15 streptomycin Uncertain significance 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
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 0.15 levofloxacin
moxifloxacin
gyrA 9033 c.1732C>A synonymous_variant 0.9 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491232 c.450T>C synonymous_variant 0.13 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 620778 c.888T>C synonymous_variant 0.2 capreomycin
amikacin
kanamycin
ccsA 620787 c.897C>G synonymous_variant 0.22 capreomycin
amikacin
kanamycin
ccsA 620793 c.903G>C synonymous_variant 0.2 capreomycin
amikacin
kanamycin
Rv0565c 657081 c.390G>A synonymous_variant 0.94 ethionamide Not assoc w R - Interim
nusG 734451 c.198G>C synonymous_variant 0.14 rifampicin
nusG 734454 c.201A>G synonymous_variant 0.14 rifampicin
nusG 734460 c.207G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
nusG 734532 c.279A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
nusG 734541 c.288A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
nusG 734553 c.300C>G synonymous_variant 0.17 rifampicin
nusG 734556 c.303C>T synonymous_variant 0.18 rifampicin
nusG 734559 c.306T>C synonymous_variant 0.18 rifampicin
nusG 734870 p.Ser206Asn missense_variant 0.15 rifampicin
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 760112 c.306T>C synonymous_variant 0.14 rifampicin
rpoB 760118 c.312T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760130 p.Asp108Glu missense_variant 0.19 rifampicin Uncertain significance
rpoB 760139 c.333A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760142 c.336C>G synonymous_variant 0.17 rifampicin
rpoB 760184 c.378A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760328 c.522G>C synonymous_variant 0.15 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.16 rifampicin
rpoB 760406 c.600G>C synonymous_variant 0.14 rifampicin
rpoB 760424 c.618C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760451 c.645C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760611 c.805T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763807 c.438T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763816 c.447C>G synonymous_variant 0.15 rifampicin
rpoC 763822 c.453C>G synonymous_variant 0.16 rifampicin
rpoC 763825 c.456G>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763828 c.459C>G synonymous_variant 0.16 rifampicin
rpoC 764188 c.819A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764195 p.Ser276Asn missense_variant 0.16 rifampicin
rpoC 764203 c.834G>T synonymous_variant 0.16 rifampicin
rpoC 764206 p.Asp279Glu missense_variant 0.16 rifampicin
rpoC 764209 c.840C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764217 p.Asn283Ser missense_variant 0.17 rifampicin
rpoC 764227 c.858G>C synonymous_variant 0.17 rifampicin
rpoC 764245 c.876C>T synonymous_variant 0.18 rifampicin
rpoC 764428 c.1059G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764431 c.1062G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.14 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.13 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764503 c.1134G>C synonymous_variant 0.17 rifampicin
rpoC 764521 c.1152T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.18 rifampicin
rpoC 764548 c.1179G>A synonymous_variant 0.18 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764716 c.1347G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 765356 p.Met663Val missense_variant 0.12 rifampicin
rpoC 765370 c.2001G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765383 p.Met672Leu missense_variant 0.16 rifampicin Uncertain significance
rpoC 765394 c.2025G>A synonymous_variant 0.14 rifampicin
rpoC 765409 c.2040T>C synonymous_variant 0.16 rifampicin
rpoC 765412 c.2043T>C synonymous_variant 0.16 rifampicin
rpoC 765421 c.2052C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765547 c.2178C>A synonymous_variant 0.14 rifampicin
rpoC 765556 c.2187G>C synonymous_variant 0.14 rifampicin
rpoC 765676 c.2307G>A synonymous_variant 0.14 rifampicin
rpoC 765688 c.2319G>C synonymous_variant 0.16 rifampicin
rpoC 765694 c.2325G>C synonymous_variant 0.16 rifampicin
rpoC 765700 c.2331T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765734 c.2365T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765865 c.2496C>T synonymous_variant 0.15 rifampicin
rpoC 765871 c.2502T>C synonymous_variant 0.16 rifampicin
rpoC 765875 p.Val836Ile missense_variant 0.18 rifampicin Uncertain significance
rpoC 765883 c.2514C>G synonymous_variant 0.15 rifampicin
rpoC 765886 c.2517C>G synonymous_variant 0.15 rifampicin
rpoC 765892 c.2523T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765946 c.2577C>T synonymous_variant 0.15 rifampicin
rpoC 766480 c.3111C>G synonymous_variant 0.13 rifampicin
rpoC 766484 c.3115_3117delGTAinsAC frameshift_variant&missense_variant 0.13 rifampicin
rpoC 766495 c.3126C>G synonymous_variant 0.18 rifampicin
rpoC 766522 c.3153C>T synonymous_variant 0.19 rifampicin
rpoC 766525 c.3156G>T synonymous_variant 0.2 rifampicin
rpoC 766528 c.3159T>C synonymous_variant 0.19 rifampicin
rpoC 766549 c.3180G>C synonymous_variant 0.2 rifampicin
rpoC 766558 c.3189G>A synonymous_variant 0.2 rifampicin
rpoC 766564 c.3195C>T synonymous_variant 0.15 rifampicin
rpoC 766565 p.Ile1066Val missense_variant 0.15 rifampicin Uncertain significance
rpoC 766573 c.3204T>C synonymous_variant 0.17 rifampicin
rpoC 766585 c.3216T>C synonymous_variant 0.21 rifampicin
rpoC 766607 c.3238_3240delATCinsCG frameshift_variant&missense_variant 0.17 rifampicin
rpoC 766618 c.3249G>T synonymous_variant 0.15 rifampicin
rpoC 766624 c.3255G>C synonymous_variant 0.14 rifampicin
rpoC 766645 c.3276A>G synonymous_variant 0.15 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.15 rifampicin
rpoC 766667 p.Ser1100Ala missense_variant 0.18 rifampicin Uncertain significance
rpoC 766672 c.3303T>C synonymous_variant 0.17 rifampicin
rpoC 766726 c.3357T>C synonymous_variant 0.19 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.21 rifampicin
rpoC 766750 c.3381C>G synonymous_variant 0.21 rifampicin
rpoC 766753 c.3384C>T synonymous_variant 0.23 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.21 rifampicin
rpoC 766798 c.3429C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766804 c.3435A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766843 c.3474T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766894 c.3525T>C synonymous_variant 0.13 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.13 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767059 c.3690T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 767098 c.3729T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 767152 c.3783T>G synonymous_variant 0.19 rifampicin
rpoC 767155 c.3786C>G synonymous_variant 0.17 rifampicin
rpoC 767167 c.3798C>T synonymous_variant 0.19 rifampicin
rpoC 767180 p.Ala1271Gln missense_variant 0.17 rifampicin
rpoC 767191 c.3822C>G 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781703 c.144G>T synonymous_variant 0.14 streptomycin
rplC 800612 c.-197A>G upstream_gene_variant 0.15 linezolid
rplC 800690 c.-119C>G upstream_gene_variant 0.18 linezolid
rplC 800703 c.-106_-104delTTGinsCC upstream_gene_variant 0.15 linezolid
rplC 800715 c.-94A>C upstream_gene_variant 0.15 linezolid
rplC 800720 c.-89T>C upstream_gene_variant 0.17 linezolid
rplC 800723 c.-86C>G upstream_gene_variant 0.16 linezolid
rplC 800747 c.-62C>G upstream_gene_variant 0.22 linezolid
rplC 800759 c.-50C>T upstream_gene_variant 0.2 linezolid
rplC 800771 c.-38C>T upstream_gene_variant 0.19 linezolid
rplC 800829 c.21C>G synonymous_variant 0.13 linezolid
rplC 800844 c.36T>C synonymous_variant 0.13 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
Rv1129c 1254589 c.-55C>T upstream_gene_variant 1.0 moxifloxacin
levofloxacin
rifampicin
isoniazid
fbiC 1303545 c.615A>G synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303584 c.654C>G synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1303590 c.660A>G synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1303614 c.684C>G synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1303623 c.693C>T synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1303632 c.702T>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303641 c.711C>T synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303650 c.720G>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303654 c.724C>T synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1303661 p.Val244Ala missense_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303695 c.765T>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303704 c.774T>G synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303713 c.783C>G synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303722 c.792C>T synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1303731 c.801A>G synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303732 p.Ser268Ala missense_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303740 c.810C>G synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303746 c.816T>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1303752 c.822A>G synonymous_variant 0.14 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1303785 c.855G>C synonymous_variant 0.16 clofazimine
pretomanid
delamanid
fbiC 1303791 c.861C>T synonymous_variant 0.16 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fbiC 1303794 c.864A>G synonymous_variant 0.14 clofazimine
pretomanid
delamanid
sigE 1364839 c.427T>C synonymous_variant 0.14 pyrazinamide
sigE 1364847 c.435G>C synonymous_variant 0.16 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 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 1471984 n.139T>A non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472019 n.174G>A non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472030 n.185G>A non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472034 n.189T>C non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472053 n.211_212delGC non_coding_transcript_exon_variant 0.14 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472314 n.469A>G non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472315 n.470T>C non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472755 n.910G>A non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475443 n.1786G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475988 n.2331A>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1476040 n.2383C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476049 n.2392C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673991 c.-211C>T upstream_gene_variant 0.14 ethionamide
isoniazid
inhA 1674015 c.-187C>G upstream_gene_variant 0.13 ethionamide
isoniazid
rpsA 1833856 c.315A>G synonymous_variant 0.14 pyrazinamide
rpsA 1833859 c.318C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.12 pyrazinamide
rpsA 1834102 c.561T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834123 c.582C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834189 c.648G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834264 c.723G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834297 c.756C>G synonymous_variant 0.18 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.16 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.2 pyrazinamide Not assoc w R - Interim
rpsA 1834396 c.855G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834456 c.915T>G synonymous_variant 0.2 pyrazinamide
rpsA 1834459 c.918G>C synonymous_variant 0.21 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.21 pyrazinamide
rpsA 1834477 c.936C>A synonymous_variant 0.19 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834499 c.958C>T synonymous_variant 0.15 pyrazinamide
rpsA 1834507 c.966C>T synonymous_variant 0.13 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834534 c.993C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.13 pyrazinamide
rpsA 1834654 c.1113G>A synonymous_variant 0.15 pyrazinamide
rpsA 1834666 c.1125G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834669 c.1128G>C synonymous_variant 0.16 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
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 2222460 c.704delT frameshift_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
kasA 2518795 c.681C>G synonymous_variant 0.13 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.98 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2477c 2783605 c.438T>C synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783929 c.114C>T synonymous_variant 0.16 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin Not assoc w R - Interim
amikacin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625525 c.-615G>C upstream_gene_variant 0.13 bedaquiline
rifampicin
lpqB 3625528 c.-618G>C upstream_gene_variant 0.13 bedaquiline
rifampicin
lpqB 3625675 c.-765G>C upstream_gene_variant 0.12 bedaquiline
rifampicin
mtrB 3625720 c.894G>C synonymous_variant 0.18 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625723 c.-813C>T upstream_gene_variant 0.19 bedaquiline
rifampicin
lpqB 3625731 c.-821C>T upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3625744 c.870G>A synonymous_variant 0.22 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625747 c.867G>C synonymous_variant 0.21 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625753 c.859_861delGCCinsAT frameshift_variant&missense_variant 0.2 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625765 c.849C>G synonymous_variant 0.2 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625774 c.840G>A synonymous_variant 0.19 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625806 c.808A>C synonymous_variant 0.18 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625807 c.807C>G synonymous_variant 0.18 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625828 c.-918G>C upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrB 3625852 c.762A>G synonymous_variant 0.18 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625867 c.747A>G synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625885 c.-975G>C upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrA 3626846 c.504G>A synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626849 c.-236C>G upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3626858 c.-245A>G upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrB 3626866 c.-253T>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3626876 c.-263A>G upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3626885 c.-272A>G upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrB 3626890 c.-277T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626891 c.-278G>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626972 c.-359A>G upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3626999 c.-386G>C upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3627008 c.-395G>C upstream_gene_variant 0.14 bedaquiline
rifampicin
fbiA 3640291 c.-252T>C upstream_gene_variant 0.19 clofazimine
pretomanid
delamanid
fbiA 3640302 c.-241T>A upstream_gene_variant 0.14 clofazimine
pretomanid
delamanid
fbiA 3640304 c.-239_-238delAAinsG upstream_gene_variant 0.14 clofazimine
pretomanid
delamanid
fbiB 3640560 c.-975G>A upstream_gene_variant 0.96 clofazimine
pretomanid
delamanid
rpoA 3877569 c.939G>C synonymous_variant 0.13 rifampicin
rpoA 3878070 c.438T>C synonymous_variant 0.13 rifampicin
rpoA 3878082 c.426T>C synonymous_variant 0.15 rifampicin
rpoA 3878103 c.405A>G synonymous_variant 0.16 rifampicin
rpoA 3878106 c.402G>C synonymous_variant 0.16 rifampicin
rpoA 3878118 c.390T>C synonymous_variant 0.18 rifampicin
rpoA 3878127 c.381G>C synonymous_variant 0.2 rifampicin
rpoA 3878130 c.378C>G synonymous_variant 0.2 rifampicin
rpoA 3878141 c.365_366delGC frameshift_variant 0.19 rifampicin
rpoA 3878145 c.362_363insGT frameshift_variant 0.2 rifampicin
rpoA 3878295 c.213A>G synonymous_variant 0.17 rifampicin
rpoA 3878298 c.210A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878742 c.-235G>A upstream_gene_variant 0.2 rifampicin
rpoA 3878746 c.-239A>G upstream_gene_variant 0.23 rifampicin Uncertain significance
rpoA 3878764 c.-257A>G upstream_gene_variant 0.28 rifampicin
rpoA 3878767 c.-260G>T upstream_gene_variant 0.31 rifampicin
rpoA 3878785 c.-278T>C upstream_gene_variant 0.32 rifampicin
rpoA 3878788 c.-281G>C upstream_gene_variant 0.31 rifampicin Uncertain significance
rpoA 3878797 c.-290G>C upstream_gene_variant 0.28 rifampicin
rpoA 3878806 c.-299C>G upstream_gene_variant 0.29 rifampicin
rpoA 3878809 c.-302T>C upstream_gene_variant 0.28 rifampicin
rpoA 3878833 c.-326C>G upstream_gene_variant 0.24 rifampicin
rpoA 3878853 c.-346G>A upstream_gene_variant 0.2 rifampicin
rpoA 3878908 c.-403_-401delAACinsTCG upstream_gene_variant 0.14 rifampicin
rpoA 3878917 c.-410G>C upstream_gene_variant 0.15 rifampicin
clpC1 4038236 c.2467_2469delACCinsGG frameshift_variant&missense_variant 0.15 pyrazinamide
clpC1 4038239 c.2466T>A synonymous_variant 0.17 pyrazinamide
clpC1 4038266 c.2439C>T synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038270 p.Pro812Ser missense_variant 0.14 pyrazinamide
clpC1 4038272 c.2433T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038275 c.2430A>G synonymous_variant 0.17 pyrazinamide
clpC1 4038278 c.2427T>C synonymous_variant 0.17 pyrazinamide
clpC1 4038293 c.2412G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038761 c.1944C>T synonymous_variant 0.13 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.22 pyrazinamide
clpC1 4038815 c.1890G>C synonymous_variant 0.22 pyrazinamide
clpC1 4039076 c.1629G>A synonymous_variant 0.21 pyrazinamide
clpC1 4039370 c.1335G>A synonymous_variant 0.15 pyrazinamide
clpC1 4039382 c.1323C>T synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4039391 c.1314T>G synonymous_variant 0.13 pyrazinamide
clpC1 4039430 c.1275T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039439 c.1266C>T synonymous_variant 0.17 pyrazinamide
clpC1 4039442 c.1263A>G synonymous_variant 0.18 pyrazinamide
clpC1 4039463 c.1242C>G synonymous_variant 0.25 pyrazinamide
clpC1 4039466 c.1239T>C synonymous_variant 0.25 pyrazinamide
clpC1 4039469 c.1236T>C synonymous_variant 0.27 pyrazinamide
clpC1 4039481 c.1224T>C synonymous_variant 0.3 pyrazinamide
clpC1 4039484 c.1221T>C synonymous_variant 0.29 pyrazinamide
clpC1 4039487 c.1218G>C synonymous_variant 0.27 pyrazinamide
clpC1 4039517 c.1188C>G synonymous_variant 0.26 pyrazinamide
clpC1 4039661 c.1044T>C synonymous_variant 0.25 pyrazinamide
clpC1 4039691 c.1014G>C synonymous_variant 0.25 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.15 pyrazinamide
clpC1 4039733 c.972G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039985 c.720G>A synonymous_variant 0.19 pyrazinamide
clpC1 4040009 c.696C>G synonymous_variant 0.2 pyrazinamide
clpC1 4040015 c.690G>T synonymous_variant 0.19 pyrazinamide
clpC1 4040018 c.687G>C synonymous_variant 0.18 pyrazinamide
clpC1 4040030 c.675C>G synonymous_variant 0.2 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.19 pyrazinamide
panD 4044703 c.-422C>G upstream_gene_variant 1.0 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide
glpK 4138451 c.1305T>C synonymous_variant 0.13 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 4138457 c.1299C>T synonymous_variant 0.13 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4138478 c.1278T>C synonymous_variant 0.14 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4138481 c.1275G>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138502 c.1254T>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138505 c.1251T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138511 c.1245C>T synonymous_variant 0.15 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 4138514 c.1242A>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138622 c.1134C>T synonymous_variant 1.0 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138714 p.Ala348Ser missense_variant 0.26 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138718 c.1038T>C synonymous_variant 0.24 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138726 p.Ala344Ser missense_variant 0.22 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138747 c.1009C>T synonymous_variant 0.22 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138751 c.1005T>C synonymous_variant 0.22 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138754 c.1002C>T synonymous_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138775 c.981C>T synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138778 c.978C>G synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138793 c.963T>C synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4138799 c.957T>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139195 c.561G>A synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139198 c.558C>G synonymous_variant 0.16 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4139609 c.147C>A synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139615 p.Glu47Asp missense_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240765 c.903C>G synonymous_variant 0.15 ethambutol
embC 4240777 c.915G>A synonymous_variant 0.16 ethambutol Not assoc w R - Interim
embC 4240780 c.918T>C synonymous_variant 0.16 ethambutol
embC 4240783 c.921G>C synonymous_variant 0.16 ethambutol
embC 4240789 c.927T>C synonymous_variant 0.17 ethambutol
embC 4240795 c.933C>G synonymous_variant 0.18 ethambutol
embC 4240819 c.957A>G synonymous_variant 0.17 ethambutol
embC 4240831 c.969T>G synonymous_variant 0.17 ethambutol
embC 4242075 p.Arg738Gln missense_variant 0.97 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245128 c.1896G>C synonymous_variant 0.14 ethambutol
embA 4245137 c.1905T>C synonymous_variant 0.14 ethambutol
embA 4245167 c.1935G>C synonymous_variant 0.13 ethambutol
embB 4248305 c.1792C>T synonymous_variant 0.21 ethambutol
embB 4248316 c.1803C>G synonymous_variant 0.21 ethambutol
embB 4248319 c.1806A>G synonymous_variant 0.18 ethambutol
embB 4248322 c.1809G>T synonymous_variant 0.18 ethambutol
embB 4248334 c.1821C>G synonymous_variant 0.18 ethambutol
embB 4248338 c.1825C>T synonymous_variant 0.17 ethambutol
embB 4249276 c.2763A>C synonymous_variant 0.16 ethambutol
embB 4249282 c.2769A>C synonymous_variant 0.15 ethambutol
embB 4249321 c.2808A>G synonymous_variant 0.19 ethambutol
embB 4249323 p.Ala937Asp missense_variant 0.19 ethambutol
embB 4249339 c.2826T>C synonymous_variant 0.17 ethambutol
embB 4249369 c.2856T>C synonymous_variant 0.16 ethambutol
embB 4249376 c.2863C>T synonymous_variant 0.18 ethambutol
embB 4249381 c.2868A>G synonymous_variant 0.19 ethambutol
embB 4249396 c.2883C>T synonymous_variant 0.18 ethambutol
embB 4249429 c.2916C>G synonymous_variant 0.14 ethambutol
ubiA 4269903 c.-70C>T upstream_gene_variant 1.0 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