TB-Profiler result

Run: SRR6785413
Summary

Run ID: SRR6785413

Sample name:

Date: 2024-03-24T17:34:56.110262

Number of reads: 2683619

Percentage reads mapped: 82.94

Median coverage: 63.0

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 0.99
lineage2.2 East-Asian (Beijing) RD105;RD207 0.97
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 rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
Drug resistance-Associated Mutations: This table reports mutations found in candidate resistance genes which have been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence Comment
rpsL 781822 p.Lys88Arg missense_variant 0.78 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
gyrB 6256 c.1017G>A synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrB 6268 c.1029C>G synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 6616 c.-686A>G upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 6622 c.-680C>T upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 6634 c.-668T>C upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6637 c.-665T>G upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6640 c.-662A>G upstream_gene_variant 0.21 levofloxacin
moxifloxacin
gyrA 6649 c.-653T>C upstream_gene_variant 0.22 levofloxacin
moxifloxacin
gyrA 6655 c.-647T>C upstream_gene_variant 0.22 levofloxacin
moxifloxacin
gyrA 6670 c.-632G>C upstream_gene_variant 0.22 levofloxacin
moxifloxacin
gyrA 6673 c.-629A>C upstream_gene_variant 0.23 levofloxacin
moxifloxacin
gyrA 6676 c.-626T>G upstream_gene_variant 0.23 levofloxacin
moxifloxacin
gyrA 6700 c.-602T>C upstream_gene_variant 0.2 levofloxacin
moxifloxacin
gyrA 6703 c.-599G>C upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6709 c.-593A>G upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrA 6712 c.-590G>C upstream_gene_variant 0.18 levofloxacin
moxifloxacin
gyrB 6728 c.1489_1491delCTAinsTG frameshift_variant&stop_gained 0.15 levofloxacin Uncertain significance
moxifloxacin
gyrA 7007 c.-295C>T upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 7010 c.-292C>T upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 7033 c.-269G>C upstream_gene_variant 0.19 levofloxacin
moxifloxacin
gyrB 7051 p.Glu604Asp missense_variant 0.2 levofloxacin
moxifloxacin
gyrA 7066 c.-236G>C upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 7084 c.-218A>G upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 7090 c.-212C>T upstream_gene_variant 0.16 levofloxacin
moxifloxacin
gyrA 7093 c.-209T>G upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 7099 c.-203G>A upstream_gene_variant 0.14 levofloxacin
moxifloxacin
gyrA 7108 c.-194G>A upstream_gene_variant 0.18 levofloxacin
moxifloxacin
gyrA 7114 c.-188C>A upstream_gene_variant 0.18 levofloxacin
moxifloxacin
gyrB 7124 c.1885_1887delTCGinsAC frameshift_variant&missense_variant 0.17 levofloxacin Uncertain significance
moxifloxacin
gyrA 7129 c.-173T>C upstream_gene_variant 0.15 levofloxacin
moxifloxacin
gyrA 7132 c.-170T>G upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrA 7141 c.-161T>C upstream_gene_variant 0.17 levofloxacin
moxifloxacin
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 7637 c.336C>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 7664 c.363T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7670 c.369A>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8642 c.1341A>G synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491173 c.391C>A synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491191 p.Gly137Arg missense_variant 0.14 clofazimine
pretomanid
delamanid
fgd1 491232 c.450T>C synonymous_variant 0.17 clofazimine
pretomanid
delamanid
fgd1 491241 p.Asp153Glu missense_variant 0.19 clofazimine
pretomanid
delamanid
fgd1 491244 c.462T>C synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fgd1 491742 c.960T>C synonymous_variant 0.98 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 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
hadA 731708 c.-222G>C upstream_gene_variant 0.15 isoniazid
hadA 731710 c.-220A>T upstream_gene_variant 0.15 isoniazid
hadA 731711 c.-219T>C upstream_gene_variant 0.15 isoniazid
hadA 731717 c.-213T>G upstream_gene_variant 0.15 isoniazid
hadA 731732 c.-198G>A upstream_gene_variant 0.17 isoniazid
hadA 731747 c.-183T>C upstream_gene_variant 0.17 isoniazid
hadA 732396 p.Gly156Ala missense_variant 0.17 isoniazid
hadA 732398 p.Ala157Thr missense_variant 0.17 isoniazid
nusG 734442 c.189G>A synonymous_variant 0.14 rifampicin
nusG 734451 c.198G>C synonymous_variant 0.13 rifampicin
nusG 734457 c.204C>G synonymous_variant 0.13 rifampicin
rpoB 760196 c.390C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.15 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760307 c.501T>C synonymous_variant 0.15 rifampicin
rpoB 760310 c.504G>C synonymous_variant 0.15 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.14 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760361 c.555T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760370 c.564C>G synonymous_variant 0.14 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760982 c.1176G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.17 rifampicin
rpoB 761006 c.1200C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.2 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761102 c.1296A>G synonymous_variant 0.16 rifampicin
rpoB 761129 c.1323G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761132 c.1326G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761180 c.1374A>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761189 c.1383T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761195 c.1389G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761207 c.1401C>T synonymous_variant 0.15 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.15 rifampicin
rpoB 761219 c.1413G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761306 c.1500C>G synonymous_variant 0.17 rifampicin
rpoB 761573 c.1767C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 762989 c.-381G>C upstream_gene_variant 0.14 rifampicin
rpoB 762995 c.3189G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.18 rifampicin
rpoB 763028 c.3222T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.98 rifampicin Not assoc w R
rpoB 763034 c.3228C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 763085 c.3279C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763148 c.-222G>C upstream_gene_variant 0.15 rifampicin
rpoC 763158 c.-212C>T upstream_gene_variant 0.15 rifampicin
rpoC 763402 c.33C>G synonymous_variant 0.14 rifampicin
rpoC 763411 c.42T>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763414 c.45T>C synonymous_variant 0.15 rifampicin
rpoC 763441 c.72C>T synonymous_variant 0.22 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.26 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763570 c.201G>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 763573 c.204G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.28 rifampicin
rpoC 763660 c.291T>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 763696 c.327T>C synonymous_variant 0.34 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.27 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.27 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.25 rifampicin
rpoC 763744 c.375G>C synonymous_variant 0.26 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.24 rifampicin
rpoC 763774 c.405G>C synonymous_variant 0.24 rifampicin
rpoC 763807 c.438T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 763816 c.447C>G synonymous_variant 0.21 rifampicin
rpoC 763835 p.Ala156Met missense_variant 0.22 rifampicin
rpoC 763853 p.Val162Ile missense_variant 0.23 rifampicin
rpoC 763891 c.522G>C synonymous_variant 0.22 rifampicin
rpoC 763894 c.525A>G synonymous_variant 0.21 rifampicin
rpoC 763900 c.531G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 763948 c.579G>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763949 c.580C>A synonymous_variant 0.14 rifampicin
rpoC 763954 c.585C>G synonymous_variant 0.14 rifampicin
rpoC 764257 c.888G>C synonymous_variant 0.15 rifampicin
rpoC 764266 c.897T>C synonymous_variant 0.15 rifampicin
rpoC 764269 c.900G>C synonymous_variant 0.16 rifampicin
rpoC 764272 c.903G>C synonymous_variant 0.17 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764353 c.984G>C synonymous_variant 0.19 rifampicin
rpoC 764365 c.996C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764380 c.1011G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764381 c.1012_1013delTCinsAG synonymous_variant 0.16 rifampicin
rpoC 764387 c.1018_1020delTTGinsCC frameshift_variant&missense_variant 0.17 rifampicin
rpoC 764405 c.1036A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764419 c.1050C>G synonymous_variant 0.13 rifampicin
rpoC 764428 c.1059G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764431 c.1062G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.18 rifampicin
rpoC 764449 c.1080G>C synonymous_variant 0.17 rifampicin
rpoC 764452 c.1083T>C synonymous_variant 0.17 rifampicin
rpoC 764458 c.1089G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764489 c.1120C>T synonymous_variant 0.17 rifampicin
rpoC 764510 c.1141C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>C synonymous_variant 0.18 rifampicin
rpoC 764539 c.1170C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764554 c.1185C>T synonymous_variant 0.19 rifampicin
rpoC 764560 c.1191T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.22 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.22 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>C synonymous_variant 0.17 rifampicin
rpoC 764651 c.1282_1284delTCGinsAGC synonymous_variant 0.17 rifampicin
rpoC 764858 c.1489T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764872 c.1503A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764932 c.1563C>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 764935 c.1566T>C synonymous_variant 0.14 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764995 c.1626C>G synonymous_variant 0.16 rifampicin Not assoc w R
rpoC 765019 c.1650A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765034 c.1665T>C synonymous_variant 0.15 rifampicin
rpoC 765040 c.1671T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765047 c.1678T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765053 c.1684_1685delTCinsAG synonymous_variant 0.15 rifampicin
rpoC 765404 p.Leu679Val missense_variant 0.14 rifampicin
rpoC 765409 c.2040T>C synonymous_variant 0.16 rifampicin
rpoC 766021 c.2652G>C synonymous_variant 0.13 rifampicin
rpoC 766027 c.2658G>C synonymous_variant 0.13 rifampicin
rpoC 766054 c.2685C>G synonymous_variant 0.14 rifampicin
rpoC 766528 c.3159T>C synonymous_variant 0.17 rifampicin
rpoC 766531 c.3162G>C synonymous_variant 0.17 rifampicin
rpoC 766540 p.Asp1057Glu missense_variant 0.16 rifampicin
rpoC 766573 c.3204T>C synonymous_variant 0.17 rifampicin
rpoC 766582 c.3213C>G synonymous_variant 0.15 rifampicin
rpoC 766583 c.3214_3216delGGTinsAC frameshift_variant&missense_variant 0.15 rifampicin
rpoC 766591 c.3222A>G synonymous_variant 0.15 rifampicin
rpoC 766594 c.3225G>C synonymous_variant 0.15 rifampicin
rpoC 766597 c.3228C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766607 p.Ile1080Leu missense_variant 0.18 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.22 rifampicin
rpoC 766645 p.Glu1092Asp missense_variant 0.87 rifampicin Not assoc w R
rpoC 766726 c.3357T>C synonymous_variant 0.18 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.22 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.24 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.19 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766861 c.3492G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.22 rifampicin
rpoC 766894 c.3525T>C synonymous_variant 0.22 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.23 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.25 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.21 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 767033 p.Ser1222Arg missense_variant 0.16 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.16 rifampicin
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 0.98 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.98 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.96 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781808 c.249C>T synonymous_variant 0.17 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.17 streptomycin
rpsL 781832 c.273T>C synonymous_variant 0.16 streptomycin
rpsL 781838 c.279G>C synonymous_variant 0.16 streptomycin
rpsL 781841 c.282C>G synonymous_variant 0.17 streptomycin
rpsL 781929 p.Gly124Ser missense_variant 0.13 streptomycin Uncertain significance
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
sigE 1364706 c.294G>A synonymous_variant 0.98 pyrazinamide Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.97 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473290 n.1445C>T non_coding_transcript_exon_variant 0.16 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1473943 n.286G>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475206 n.1549C>T non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475209 n.1552G>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475369 n.1712G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid Uncertain significance
rrl 1475608 n.1951T>C non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid
rrl 1475638 n.1981C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475642 n.1985T>C non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475657 n.2000A>G non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475659 n.2002G>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1476214 n.2557G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833724 c.183C>G synonymous_variant 0.13 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.15 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833748 c.207C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.14 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.14 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.15 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.14 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.15 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.16 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.98 pyrazinamide Not assoc w R - Interim
rpsA 1834348 c.807T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
rpsA 1834396 c.855G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834465 c.924T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.15 pyrazinamide
rpsA 1834540 c.999G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.21 pyrazinamide
rpsA 1834618 c.1077G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.2 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.25 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
bacA 2063790 c.939A>G synonymous_variant 0.98 streptomycin Not assoc w R - Interim
kanamycin
capreomycin
amikacin
katG 2154724 p.Arg463Leu missense_variant 0.99 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
Rv2477c 2782912 p.Ser377Thr missense_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782927 p.Thr372Glu missense_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782936 c.1107G>T synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782948 c.1095A>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783140 c.903C>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783149 c.894G>C synonymous_variant 0.14 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 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 2783656 c.387G>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783665 c.378A>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783700 p.Thr115Ser missense_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783718 c.325T>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783719 c.324A>G synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783751 p.Ile98Val missense_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783758 p.Asp95Glu missense_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783761 c.282G>C synonymous_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783766 p.Met93Leu missense_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783776 c.267G>C synonymous_variant 0.19 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783779 c.264T>C synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783797 p.Asp82Glu missense_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783822 p.Gln74Leu missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783833 c.210G>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783839 c.204C>G synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783843 p.Gly67Asp missense_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783846 p.Thr66Asn missense_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783860 c.183T>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783863 c.180C>T synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783883 c.160T>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783884 c.159T>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783887 c.156C>G synonymous_variant 0.2 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783914 c.129T>C synonymous_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783920 c.123G>C synonymous_variant 0.24 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783929 c.114C>G synonymous_variant 0.21 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
thyX 3067391 c.555G>C synonymous_variant 0.14 para-aminosalicylic_acid
thyX 3067394 c.552G>C synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067439 c.507A>G synonymous_variant 0.22 para-aminosalicylic_acid
thyX 3067445 c.501C>G synonymous_variant 0.21 para-aminosalicylic_acid
thyX 3067457 c.489C>G synonymous_variant 0.21 para-aminosalicylic_acid
thyX 3067465 p.Ile161Val missense_variant 0.2 para-aminosalicylic_acid
thyX 3067475 c.471A>G synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067490 c.456C>G synonymous_variant 0.19 para-aminosalicylic_acid
thyX 3067493 c.453A>G synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067515 p.Ser144Thr missense_variant 0.23 para-aminosalicylic_acid
thyX 3067583 c.363C>G synonymous_variant 0.21 para-aminosalicylic_acid
thyX 3067718 c.228C>G synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067721 c.225T>C synonymous_variant 0.17 para-aminosalicylic_acid
thyX 3067727 c.219A>C synonymous_variant 0.15 para-aminosalicylic_acid
thyX 3067736 c.208_210delTTCinsCT frameshift_variant&missense_variant 0.14 para-aminosalicylic_acid
thyX 3067739 c.207T>C synonymous_variant 0.14 para-aminosalicylic_acid
thyX 3067761 p.Arg62Lys missense_variant 0.15 para-aminosalicylic_acid
thyX 3067765 p.Leu61Ile missense_variant 0.14 para-aminosalicylic_acid
thyX 3067772 c.174C>G synonymous_variant 0.14 para-aminosalicylic_acid
thyX 3067781 c.165C>A synonymous_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
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625225 c.-315G>C upstream_gene_variant 0.16 bedaquiline
rifampicin
lpqB 3625549 c.-639G>A upstream_gene_variant 0.23 bedaquiline
rifampicin
mtrB 3625569 c.1045T>C synonymous_variant 0.21 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625572 p.Thr348Ser missense_variant 0.2 bedaquiline
rifampicin
lpqB 3625579 c.-669A>G upstream_gene_variant 0.2 bedaquiline
rifampicin
lpqB 3625594 c.-684T>C upstream_gene_variant 0.22 bedaquiline
rifampicin
lpqB 3625602 c.-692T>C upstream_gene_variant 0.23 bedaquiline
rifampicin
lpqB 3625612 c.-702G>C upstream_gene_variant 0.25 bedaquiline
rifampicin
mtrB 3625616 p.Arg333Ala missense_variant 0.27 bedaquiline
rifampicin
lpqB 3625624 c.-714C>G upstream_gene_variant 0.24 bedaquiline
rifampicin
mtrB 3625656 c.958T>C synonymous_variant 0.18 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3625663 c.-753G>C upstream_gene_variant 0.19 bedaquiline
rifampicin
lpqB 3625669 c.-759G>C upstream_gene_variant 0.18 bedaquiline
rifampicin
lpqB 3625687 c.-777G>C upstream_gene_variant 0.15 bedaquiline
rifampicin
lpqB 3625690 c.-780T>C upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrB 3625705 c.909C>G synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625714 c.-804C>T upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3625720 c.894G>C synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.98 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626930 c.-317A>G upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrB 3626957 c.-344G>C upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626972 c.-359A>G upstream_gene_variant 0.15 bedaquiline
rifampicin
rpoA 3877656 c.852T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877668 c.840A>G synonymous_variant 0.15 rifampicin
rpoA 3877679 p.Ala277Ser missense_variant 0.15 rifampicin
rpoA 3877782 c.726T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877818 c.690A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.23 rifampicin
rpoA 3877866 c.642G>C synonymous_variant 0.22 rifampicin
rpoA 3877875 c.633T>G synonymous_variant 0.22 rifampicin
rpoA 3877878 c.630G>C synonymous_variant 0.22 rifampicin
rpoA 3877890 c.618C>T synonymous_variant 0.2 rifampicin
rpoA 3877896 c.612G>C synonymous_variant 0.19 rifampicin
rpoA 3877900 p.Ser203Asn missense_variant 0.19 rifampicin
rpoA 3877905 c.603A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877909 p.Asn200Ser missense_variant 0.16 rifampicin
clpC1 4038908 c.1797C>G synonymous_variant 0.13 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.13 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.13 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.14 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4039004 c.1701C>G synonymous_variant 0.16 pyrazinamide
clpC1 4039775 c.930G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039781 c.924G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039790 c.915C>G synonymous_variant 0.15 pyrazinamide
clpC1 4039826 c.879C>G synonymous_variant 0.13 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040036 c.669C>G synonymous_variant 0.14 pyrazinamide
clpC1 4040228 c.477G>T synonymous_variant 0.12 pyrazinamide
clpC1 4040237 c.468C>T synonymous_variant 0.14 pyrazinamide
clpC1 4040246 c.459C>G synonymous_variant 0.15 pyrazinamide
clpC1 4040249 c.456A>G synonymous_variant 0.14 pyrazinamide
clpC1 4040267 c.438A>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
embC 4241488 c.1626G>C synonymous_variant 0.17 ethambutol
embC 4241496 p.Ala545Gly missense_variant 0.17 ethambutol
embC 4241500 c.1638A>C synonymous_variant 0.17 ethambutol
embC 4241501 p.Ser547Thr missense_variant 0.17 ethambutol
embC 4241506 c.1644G>C synonymous_variant 0.18 ethambutol
embC 4241518 c.1656A>G synonymous_variant 0.17 ethambutol
embC 4241521 c.1659T>C synonymous_variant 0.18 ethambutol Not assoc w R - Interim
embC 4241530 c.1668C>A synonymous_variant 0.19 ethambutol
embC 4241536 c.1674A>G synonymous_variant 0.17 ethambutol
embC 4241539 c.1677T>C synonymous_variant 0.17 ethambutol Not assoc w R - Interim
embC 4241545 c.1683T>C synonymous_variant 0.17 ethambutol
embC 4241548 c.1686T>C synonymous_variant 0.16 ethambutol
embC 4241551 c.1689A>G synonymous_variant 0.15 ethambutol
embC 4241567 p.Ile569Val missense_variant 0.18 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.98 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.97 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 0.94 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Not assoc w R