TB-Profiler result

Run: SRR25827605
Summary

Run ID: SRR25827605

Sample name:

Date: 2024-04-14T11:38:17.551516

Number of reads: 10395844

Percentage reads mapped: 96.37

Median coverage: 318.0

Strain: lineage2.2.1;lineage3;lineage4

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.19
lineage2 East-Asian RD105 0.68
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.65
lineage2.2 East-Asian (Beijing) RD105;RD207 0.68
lineage4 Euro-American None 0.14
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
rpoC p.Leu527Val Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gln497Lys Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Thr Uncertain significance Mutation from literature
rrs n.462C>T Uncertain significance Mutation from literature
gid c.441delA Assoc w R
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)
p.Ser91Pro 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
p.Ser91Pro 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 0.26 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)
gyrA 7572 p.Ser91Pro missense_variant 0.18 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)
rpoB 761155 p.Ser450Leu missense_variant 0.73 rifampicin Assoc w R
rpoC 764948 p.Leu527Val missense_variant 0.22 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.57 streptomycin Assoc w R
rpsL 781822 p.Lys88Thr missense_variant 0.17 streptomycin Uncertain significance Mutation from literature
rrs 1472307 n.462C>T non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance Mutation from literature
katG 2155168 p.Ser315Thr missense_variant 0.79 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.13 pyrazinamide Assoc w R
embB 4248002 p.Gln497Lys missense_variant 0.2 ethambutol Assoc w R
gid 4407761 c.441delA frameshift_variant 0.2 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
gyrA 7362 p.Glu21Gln missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7581 p.Asp94Ser missense_variant 0.19 levofloxacin
moxifloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8603 c.1302A>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8619 c.1318T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8624 c.1323G>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8636 c.1335A>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8642 c.1341A>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8672 c.1371A>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8693 c.1392T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8696 c.1395G>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8699 c.1398A>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8714 c.1413A>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 9248 c.1947G>C synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.35 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.86 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.65 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.14 capreomycin Not assoc w R
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.71 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.84 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.69 ethionamide Uncertain significance
hadA 731717 c.-213T>G upstream_gene_variant 0.13 isoniazid
hadA 731747 c.-183T>C upstream_gene_variant 0.15 isoniazid
rpoB 759746 c.-61C>T upstream_gene_variant 0.18 rifampicin Not assoc w R
rpoB 760118 c.312T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760139 c.333A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760142 c.336C>G synonymous_variant 0.15 rifampicin
rpoB 760181 c.375T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.18 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760283 c.477G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760307 c.501T>C synonymous_variant 0.2 rifampicin
rpoB 760310 c.504G>C synonymous_variant 0.19 rifampicin
rpoB 760328 c.522G>C synonymous_variant 0.2 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.21 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760361 c.555T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760370 c.564C>G synonymous_variant 0.19 rifampicin
rpoB 760376 p.Asp190Glu missense_variant 0.19 rifampicin Uncertain significance
rpoB 760380 p.Thr192Leu missense_variant 0.18 rifampicin
rpoB 760406 c.600G>C synonymous_variant 0.16 rifampicin
rpoB 760925 c.1119T>C synonymous_variant 0.13 rifampicin
rpoB 760931 c.1125C>G synonymous_variant 0.14 rifampicin
rpoB 760934 c.1128C>T synonymous_variant 0.14 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760982 c.1176G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.18 rifampicin
rpoB 761006 c.1200C>T synonymous_variant 0.19 rifampicin
rpoB 761015 c.1209G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761018 c.1212G>A synonymous_variant 0.2 rifampicin
rpoB 761021 c.1215G>C synonymous_variant 0.2 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761102 c.1296A>G synonymous_variant 0.14 rifampicin
rpoB 761150 c.1344A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761165 c.1359G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761189 c.1383T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761207 c.1401C>T synonymous_variant 0.17 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.18 rifampicin
rpoB 761249 c.1443A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761570 c.1764T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762329 c.2523G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762347 c.2541T>C synonymous_variant 0.14 rifampicin
rpoB 762362 p.Glu852Asp missense_variant 0.15 rifampicin
rpoB 762369 c.2563T>C synonymous_variant 0.15 rifampicin
rpoC 762398 c.-972T>C upstream_gene_variant 0.18 rifampicin
rpoC 762401 c.-969G>C upstream_gene_variant 0.17 rifampicin
rpoB 762404 c.2598T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 762410 c.-960T>C upstream_gene_variant 0.2 rifampicin
rpoB 762416 c.2610A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 762419 c.-951C>G upstream_gene_variant 0.21 rifampicin
rpoC 762434 c.-936T>C upstream_gene_variant 0.24 rifampicin
rpoB 762449 c.2643C>A synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 762467 c.-903C>T upstream_gene_variant 0.16 rifampicin
rpoB 762857 c.3051C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 762863 c.3057T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.88 rifampicin Not assoc w R
rpoC 763486 c.117T>G synonymous_variant 0.13 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.2 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.2 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.19 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.18 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.18 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.17 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763816 c.447C>G synonymous_variant 0.13 rifampicin
rpoC 763996 c.627T>C synonymous_variant 0.13 rifampicin
rpoC 764002 c.633C>T synonymous_variant 0.14 rifampicin
rpoC 764005 c.636G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764011 c.642T>C synonymous_variant 0.16 rifampicin
rpoC 764024 c.655_657delTTGinsCC frameshift_variant&missense_variant 0.17 rifampicin
rpoC 764032 p.Asp221Glu missense_variant 0.19 rifampicin
rpoC 764040 p.Ser224Thr missense_variant 0.19 rifampicin
rpoC 764044 c.675T>G synonymous_variant 0.18 rifampicin
rpoC 764059 c.690G>T synonymous_variant 0.2 rifampicin
rpoC 764083 c.714A>G synonymous_variant 0.2 rifampicin
rpoC 764098 c.729A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764101 c.732C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764102 p.Val245Ile missense_variant 0.2 rifampicin
rpoC 764110 c.741C>G synonymous_variant 0.2 rifampicin
rpoC 764112 p.Tyr248Phe missense_variant 0.2 rifampicin
rpoC 764116 c.747C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.23 rifampicin
rpoC 764140 c.771C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764188 c.819A>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764195 p.Ser276Ile missense_variant 0.26 rifampicin
rpoC 764203 c.834G>C synonymous_variant 0.25 rifampicin
rpoC 764206 c.837T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764215 c.846A>G synonymous_variant 0.27 rifampicin
rpoC 764257 c.888G>C synonymous_variant 0.26 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.23 rifampicin
rpoC 764269 c.900G>C synonymous_variant 0.24 rifampicin
rpoC 764272 c.903G>C synonymous_variant 0.25 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764293 c.924G>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764317 c.948C>G synonymous_variant 0.18 rifampicin
rpoC 764827 c.1458G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764887 c.1518G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519_1521delTTGinsCC frameshift_variant&missense_variant 0.14 rifampicin
rpoC 764893 c.1524T>C synonymous_variant 0.14 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.14 rifampicin
rpoC 764932 c.1563C>G synonymous_variant 0.13 rifampicin
rpoC 765835 c.2466C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765871 c.2502T>C synonymous_variant 0.16 rifampicin
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 765937 c.2568T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765946 c.2577C>T synonymous_variant 0.15 rifampicin
rpoC 766393 c.3024C>G synonymous_variant 0.13 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.16 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.15 rifampicin
rpoC 766674 p.Gly1102Asp missense_variant 0.15 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.13 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.16 rifampicin
rpoC 767158 c.3789T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767167 c.3798C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767180 p.Ala1271Gln missense_variant 0.15 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.14 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 0.87 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.67 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.67 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 0.99 streptomycin Not assoc w R
rpsL 781832 c.273T>C synonymous_variant 0.15 streptomycin
rpsL 781835 c.276T>C synonymous_variant 0.15 streptomycin Not assoc w R - Interim
rpsL 781838 c.279G>C synonymous_variant 0.16 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.19 streptomycin
rpsL 781865 c.306G>C synonymous_variant 0.21 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.2 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.21 streptomycin
rpsL 781877 c.318T>C synonymous_variant 0.22 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.21 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.21 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.21 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.21 streptomycin Uncertain significance
Rv1129c 1253930 p.Phe202Tyr missense_variant 0.16 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.83 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.63 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.22 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472315 n.470T>C non_coding_transcript_exon_variant 0.23 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472969 n.1124A>G non_coding_transcript_exon_variant 0.17 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472970 n.1125C>G non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472977 n.1132G>C non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472978 n.1133T>C non_coding_transcript_exon_variant 0.18 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473105 n.1260G>A non_coding_transcript_exon_variant 0.27 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.26 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.26 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473166 n.1321G>A non_coding_transcript_exon_variant 0.25 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473839 n.182G>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1473943 n.286G>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.22 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475761 n.2104_2106delCGCinsGT non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475765 n.2111delG non_coding_transcript_exon_variant 0.28 capreomycin
linezolid
rrl 1475881 n.2224T>C non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1475988 n.2331A>G non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476032 n.2375C>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1476033 n.2376T>C non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1476089 n.2432T>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476095 n.2438C>G non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1476110 n.2453G>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.24 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.25 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1476693 n.3036G>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1476716 n.3059A>C non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476726 n.3069A>G non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1476732 n.3075T>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rpsA 1833856 c.315A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.18 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.25 pyrazinamide
rpsA 1833940 c.399C>G synonymous_variant 0.26 pyrazinamide
rpsA 1833971 c.430C>T synonymous_variant 0.26 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.27 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.27 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.26 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.24 pyrazinamide
rpsA 1834096 c.555G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834099 c.558C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834102 c.561T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834108 c.567C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834117 c.576G>A synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
rpsA 1834150 c.609G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834153 c.612T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834154 c.613_615delAACinsCG frameshift_variant&missense_variant 0.14 pyrazinamide Uncertain significance
rpsA 1834157 c.616T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834162 c.621A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834165 c.624A>G synonymous_variant 0.14 pyrazinamide
rpsA 1834169 p.Thr210Ala missense_variant 0.15 pyrazinamide Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.74 pyrazinamide Not assoc w R - Interim
rpsA 1834189 c.648G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834195 c.654G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834222 c.681T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834249 c.708T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834261 c.720A>G synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
rpsA 1834264 c.723G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834297 c.756C>G synonymous_variant 0.19 pyrazinamide
rpsA 1834303 c.762T>G synonymous_variant 0.19 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1834396 c.855G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834423 c.882G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834435 c.894G>C synonymous_variant 0.16 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.19 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.19 pyrazinamide
rpsA 1834474 c.933C>G synonymous_variant 0.19 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.22 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834531 c.990C>T synonymous_variant 0.24 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.25 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.25 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.25 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.25 pyrazinamide
rpsA 1834619 c.1078T>C synonymous_variant 0.25 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.24 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.25 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.22 pyrazinamide
rpsA 1834657 c.1116G>A synonymous_variant 0.22 pyrazinamide Not assoc w R - Interim
rpsA 1834690 c.1149T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834732 c.1191T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834733 p.Ala398Ser missense_variant 0.18 pyrazinamide
rpsA 1834738 c.1197A>G synonymous_variant 0.18 pyrazinamide
rpsA 1834753 c.1212T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834759 c.1218A>C synonymous_variant 0.14 pyrazinamide
rpsA 1834765 p.Glu408Asp missense_variant 0.13 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 0.86 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.85 pyrazinamide Not assoc w R
PPE35 2168565 p.Pro683Leu missense_variant 0.19 pyrazinamide Uncertain significance
PPE35 2170599 p.Val5Ala missense_variant 0.21 pyrazinamide 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 0.24 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.2 pyrazinamide
kasA 2517917 c.-198G>C upstream_gene_variant 0.18 isoniazid
kasA 2517950 c.-165C>G upstream_gene_variant 0.16 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.2 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.17 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 2783593 c.450T>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783605 c.438T>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783611 c.432C>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783628 p.Ala139Ser missense_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783656 c.387G>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783659 c.384A>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783674 c.369T>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ribD 2986827 c.-12G>A upstream_gene_variant 0.26 para-aminosalicylic_acid
ald 3086742 c.-78A>C upstream_gene_variant 0.13 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
whiB7 3568425 c.255T>G synonymous_variant 0.15 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.66 pyrazinamide Not assoc w R - Interim
Rv3236c 3613710 c.-594G>T upstream_gene_variant 0.19 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.67 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiB 3641677 p.Val48Ala missense_variant 0.22 clofazimine
pretomanid
delamanid
rpoA 3877692 c.816G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
clpC1 4038302 c.2403C>G synonymous_variant 0.15 pyrazinamide
clpC1 4038308 c.2397G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038356 c.2349T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.14 pyrazinamide
clpC1 4038640 p.Asp689Asn missense_variant 0.17 pyrazinamide
clpC1 4038653 c.2052C>T synonymous_variant 0.16 pyrazinamide
clpC1 4038658 p.Lys683Gln missense_variant 0.14 pyrazinamide
clpC1 4038661 p.Ser682Thr missense_variant 0.15 pyrazinamide
clpC1 4038662 c.2043T>C synonymous_variant 0.13 pyrazinamide
clpC1 4038671 c.2034T>C synonymous_variant 0.17 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.18 pyrazinamide
clpC1 4038701 c.2004G>C synonymous_variant 0.18 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 0.17 pyrazinamide
clpC1 4038707 c.1998C>G synonymous_variant 0.17 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 0.17 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.17 pyrazinamide
clpC1 4038755 c.1950G>T synonymous_variant 0.17 pyrazinamide
clpC1 4038764 c.1941C>G synonymous_variant 0.15 pyrazinamide
clpC1 4038767 c.1938G>C synonymous_variant 0.15 pyrazinamide
clpC1 4038773 c.1932T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038782 c.1923G>C synonymous_variant 0.15 pyrazinamide
clpC1 4038790 c.1915C>T synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038812 c.1893T>C synonymous_variant 0.19 pyrazinamide
clpC1 4038845 c.1860G>C synonymous_variant 0.23 pyrazinamide
clpC1 4038860 c.1845G>C synonymous_variant 0.25 pyrazinamide Not assoc w R - Interim
clpC1 4038878 c.1827A>G synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
clpC1 4038908 c.1797C>G synonymous_variant 0.29 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.3 pyrazinamide
clpC1 4038923 c.1780_1782delCTAinsTG frameshift_variant&synonymous_variant 0.31 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.28 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.28 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.26 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.26 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 0.27 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.27 pyrazinamide Not assoc w R - Interim
clpC1 4039022 c.1683A>G synonymous_variant 0.25 pyrazinamide
clpC1 4039064 c.1641C>T synonymous_variant 0.19 pyrazinamide
clpC1 4039073 c.1632C>A synonymous_variant 0.18 pyrazinamide
clpC1 4039097 c.1608G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039103 c.1602T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039298 c.1407T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039319 c.1386T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4039322 c.1383T>C synonymous_variant 0.14 pyrazinamide
clpC1 4039328 c.1377A>C synonymous_variant 0.14 pyrazinamide
clpC1 4039337 c.1366_1368delACAinsCG frameshift_variant&synonymous_variant 0.14 pyrazinamide
clpC1 4039364 c.1341C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039391 c.1314T>G synonymous_variant 0.16 pyrazinamide
clpC1 4039406 c.1299G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039409 c.1296T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039412 c.1293T>G synonymous_variant 0.13 pyrazinamide
clpC1 4039415 p.Glu430Asp missense_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039517 c.1188C>G synonymous_variant 0.13 pyrazinamide
clpC1 4039556 c.1149G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039559 c.1146C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039562 c.1143C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039565 c.1140G>C synonymous_variant 0.16 pyrazinamide
clpC1 4039570 p.Met379Leu missense_variant 0.16 pyrazinamide Uncertain significance
clpC1 4039576 p.Ala377Pro missense_variant 0.16 pyrazinamide
clpC1 4039577 c.1128T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4039589 c.1116G>T synonymous_variant 0.17 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.17 pyrazinamide
clpC1 4039616 c.1089G>C synonymous_variant 0.17 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.18 pyrazinamide
embC 4241022 p.Ala387Val missense_variant 0.3 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.19 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.64 ethambutol Not assoc w R
embB 4247429 c.916_918delATGinsGA frameshift_variant&missense_variant 0.21 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.63 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 0.87 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.28 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.68 streptomycin Not assoc w R