TB-Profiler result

Run: ERR11466044
Summary

Run ID: ERR11466044

Sample name:

Date: 2024-04-14T11:32:42.521532

Number of reads: 2832802

Percentage reads mapped: 97.44

Median coverage: 63.0

Strain: lineage4.1.1.3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 1.0
lineage4.1.1.3 Euro-American (X-type) RD193 1.0
lineage4 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 1.0
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.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 1472307 n.462C>T non_coding_transcript_exon_variant 0.19 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
gyrB 4982 c.-258C>G upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 6205 c.966C>T synonymous_variant 0.14 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 7728 c.427_429delAGGinsCT frameshift_variant&missense_variant 0.2 levofloxacin
moxifloxacin
gyrA 7736 c.435C>T synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 7760 c.459C>T synonymous_variant 0.27 levofloxacin
moxifloxacin
gyrA 7763 c.462T>G synonymous_variant 0.28 levofloxacin
moxifloxacin
gyrA 7793 c.492G>C synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 7796 c.495G>C synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7799 c.498A>G synonymous_variant 0.23 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7817 c.516C>T synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7832 c.531G>T synonymous_variant 0.25 levofloxacin
moxifloxacin
gyrA 7835 c.534A>G synonymous_variant 0.25 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7838 c.537C>T synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7847 c.546G>C synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 7853 c.552C>T synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7859 c.558A>C synonymous_variant 0.21 levofloxacin
moxifloxacin
gyrA 7865 c.564T>C synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 7886 c.585T>C synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 7898 p.Asp199Glu missense_variant 0.22 levofloxacin
moxifloxacin
gyrA 7911 p.Ala204Cys missense_variant 0.18 levofloxacin
moxifloxacin
gyrA 7922 c.621T>C synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 7923 p.His208Tyr missense_variant 0.18 levofloxacin
moxifloxacin
gyrA 7942 p.Glu214Ala missense_variant 0.2 levofloxacin
moxifloxacin
gyrA 7946 c.645C>G synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 7950 p.Ala217Thr missense_variant 0.24 levofloxacin
moxifloxacin
gyrA 7955 c.654G>C synonymous_variant 0.25 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7963 p.Gly221Glu missense_variant 0.21 levofloxacin
moxifloxacin
gyrA 7992 p.Ala231Ser missense_variant 0.23 levofloxacin
moxifloxacin
gyrA 7997 c.696A>T synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 8009 c.708A>G synonymous_variant 0.22 levofloxacin
moxifloxacin
gyrA 8012 c.711C>A synonymous_variant 0.18 levofloxacin
moxifloxacin
gyrA 8020 p.Thr240Ile missense_variant 0.14 levofloxacin
moxifloxacin
gyrA 8022 c.721_723delGCTinsTC frameshift_variant&missense_variant 0.13 levofloxacin
moxifloxacin
gyrA 8036 c.735A>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8039 c.738T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8048 c.747C>T synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8054 c.753T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8057 c.756A>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8084 c.783G>A synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 8121 c.820T>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 8129 c.828T>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
mshA 575566 c.219G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 1.0 ethionamide Uncertain significance
nusG 734407 p.Val52Ile missense_variant 0.12 rifampicin
nusG 734415 c.162C>T synonymous_variant 0.15 rifampicin
nusG 734421 c.168A>G synonymous_variant 0.14 rifampicin
nusG 734424 c.171G>C synonymous_variant 0.12 rifampicin
nusG 734439 c.186C>G synonymous_variant 0.15 rifampicin
nusG 734442 c.189G>A synonymous_variant 0.14 rifampicin
nusG 734451 c.198G>C synonymous_variant 0.14 rifampicin
nusG 734454 c.201A>G synonymous_variant 0.13 rifampicin
nusG 734475 c.222T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
nusG 734505 c.252G>T synonymous_variant 0.17 rifampicin
rpoB 760406 c.600G>C synonymous_variant 0.17 rifampicin
rpoB 760412 c.606C>T synonymous_variant 0.18 rifampicin
rpoB 760418 c.612G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760424 c.618C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760433 c.627C>T synonymous_variant 0.15 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761414 c.1608A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761423 c.1617T>C synonymous_variant 0.2 rifampicin
rpoB 761435 c.1629T>C synonymous_variant 0.17 rifampicin
rpoB 761437 p.Ala544Glu missense_variant 0.16 rifampicin
rpoB 761439 p.Asp545Asn missense_variant 0.16 rifampicin
rpoB 761444 c.1638T>C synonymous_variant 0.17 rifampicin
rpoB 761447 c.1641C>G synonymous_variant 0.18 rifampicin
rpoB 761450 c.1644C>T synonymous_variant 0.18 rifampicin
rpoB 761465 c.1659G>T synonymous_variant 0.25 rifampicin
rpoB 761510 c.1704T>C synonymous_variant 0.29 rifampicin
rpoB 761537 c.1731C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761570 c.1764T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761606 c.1800C>G synonymous_variant 0.27 rifampicin
rpoB 761612 c.1806G>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764131 c.762T>C synonymous_variant 0.14 rifampicin
rpoC 764152 c.783C>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764159 c.790C>T synonymous_variant 0.13 rifampicin
rpoC 764803 c.1434C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.22 rifampicin Not assoc w R
rpoC 764812 c.1443C>G synonymous_variant 0.21 rifampicin
rpoC 764815 c.1446A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764824 c.1455T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764833 c.1464A>G synonymous_variant 0.23 rifampicin
rpoC 764836 c.1467G>A synonymous_variant 0.23 rifampicin
rpoC 764839 c.1470C>G synonymous_variant 0.23 rifampicin
rpoC 764845 c.1476C>A synonymous_variant 0.25 rifampicin
rpoC 764851 c.1482C>T synonymous_variant 0.18 rifampicin
rpoC 764854 c.1485G>T synonymous_variant 0.19 rifampicin
rpoC 764857 c.1488G>T synonymous_variant 0.19 rifampicin
rpoC 764875 c.1506C>G synonymous_variant 0.18 rifampicin
rpoC 764888 c.1519T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.17 rifampicin
rpoC 764896 c.1527C>T synonymous_variant 0.18 rifampicin
rpoC 764911 c.1542A>G synonymous_variant 0.16 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Not assoc w R
rpoC 765409 c.2040T>C synonymous_variant 0.17 rifampicin
rpoC 765412 c.2043T>C synonymous_variant 0.17 rifampicin
rpoC 765421 c.2052C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765451 c.2082C>T synonymous_variant 0.16 rifampicin
rpoC 765454 c.2085C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765478 c.2109T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765496 c.2127C>T synonymous_variant 0.15 rifampicin
rpoC 765499 c.2130C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765508 c.2139C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765934 c.2565C>G synonymous_variant 0.22 rifampicin
rpoC 765937 c.2568T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 765946 c.2577C>T synonymous_variant 0.21 rifampicin
rpoC 765947 c.2578T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 765961 c.2592G>A synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 765967 c.2598C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765994 c.2625A>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766009 c.2640G>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 766010 c.2641_2642delTCinsAG synonymous_variant 0.18 rifampicin
rpoC 766027 c.2658G>T synonymous_variant 0.16 rifampicin
rpoC 766348 c.2979A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766351 c.2982C>G synonymous_variant 0.19 rifampicin
rpoC 766381 c.3012C>T synonymous_variant 0.26 rifampicin
rpoC 766384 c.3015A>G synonymous_variant 0.3 rifampicin
rpoC 766393 c.3024C>G synonymous_variant 0.3 rifampicin
rpoC 766397 c.3028C>T synonymous_variant 0.35 rifampicin
rpoC 766408 c.3039C>T synonymous_variant 0.38 rifampicin Not assoc w R - Interim
rpoC 766426 c.3057C>T synonymous_variant 0.43 rifampicin
rpoC 766429 c.3060C>G synonymous_variant 0.43 rifampicin
rpoC 766447 c.3078T>C synonymous_variant 0.39 rifampicin
rpoC 766456 c.3087C>G synonymous_variant 0.41 rifampicin
rpoC 766459 c.3090G>T synonymous_variant 0.39 rifampicin
rpoC 766462 c.3093G>C synonymous_variant 0.4 rifampicin
rpoC 766484 c.3115_3117delGTAinsAC frameshift_variant&missense_variant 0.28 rifampicin
rpoC 766549 c.3180G>C synonymous_variant 0.13 rifampicin
rpoC 766573 c.3204T>C synonymous_variant 0.16 rifampicin
rpoC 766582 c.3213C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766585 c.3216T>C synonymous_variant 0.17 rifampicin
rpoC 766607 c.3238_3240delATCinsCG frameshift_variant&missense_variant 0.15 rifampicin
rpoC 766624 c.3255G>C synonymous_variant 0.17 rifampicin
rpoC 766645 c.3276A>G synonymous_variant 0.18 rifampicin
rpoC 766651 c.3282T>C synonymous_variant 0.2 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.2 rifampicin
rpoC 766667 p.Ser1100Ala missense_variant 0.22 rifampicin Uncertain significance
rpoC 766672 c.3303T>C synonymous_variant 0.24 rifampicin
rpoC 766714 c.3345G>C synonymous_variant 0.16 rifampicin
rpoC 766750 c.3381C>G synonymous_variant 0.2 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766774 c.3405T>C synonymous_variant 0.19 rifampicin
rpoC 766843 c.3474T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766846 c.3477C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766864 c.3495G>C synonymous_variant 0.23 rifampicin
rpoC 766894 c.3525T>C synonymous_variant 0.2 rifampicin
rpoC 766895 c.3526T>C synonymous_variant 0.2 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.2 rifampicin
rpoC 766903 c.3534C>T synonymous_variant 0.21 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.23 rifampicin
rpoC 766945 c.3576A>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 766948 c.3579G>C synonymous_variant 0.2 rifampicin
rpoC 766960 c.3591C>T synonymous_variant 0.3 rifampicin
rpoC 766972 c.3603G>C synonymous_variant 0.22 rifampicin
rpoC 766978 c.3609C>A synonymous_variant 0.24 rifampicin
rpoC 766996 c.3627C>T synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 767008 c.3639G>A synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.31 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.31 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.23 rifampicin
rpoC 767149 c.3780C>G synonymous_variant 0.19 rifampicin
rpoC 767167 c.3798C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767173 c.3804C>G synonymous_variant 0.15 rifampicin
mmpL5 775639 p.Ile948Val 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
rplC 800219 c.-590T>C upstream_gene_variant 0.9 linezolid
fbiC 1304887 c.1957C>T synonymous_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1304891 p.Ile654Thr missense_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1304895 c.1965C>G synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1304910 c.1980G>C synonymous_variant 0.18 clofazimine
pretomanid
delamanid
fbiC 1304916 c.1986T>C synonymous_variant 0.17 clofazimine
pretomanid
delamanid
sigE 1364868 c.456T>C synonymous_variant 0.14 pyrazinamide
sigE 1364874 c.462C>T synonymous_variant 0.14 pyrazinamide
sigE 1364877 c.465G>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
sigE 1364887 c.475_477delTTAinsCG frameshift_variant&missense_variant 0.18 pyrazinamide Uncertain significance
sigE 1364892 c.480C>G synonymous_variant 0.17 pyrazinamide
sigE 1364901 c.489C>T synonymous_variant 0.17 pyrazinamide
sigE 1364913 c.501C>G synonymous_variant 0.18 pyrazinamide
sigE 1364919 c.507T>C synonymous_variant 0.17 pyrazinamide
sigE 1364925 c.513C>G synonymous_variant 0.17 pyrazinamide
sigE 1364931 c.519C>G synonymous_variant 0.19 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.33 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472306 n.461T>G non_coding_transcript_exon_variant 0.19 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472314 n.469A>G non_coding_transcript_exon_variant 0.17 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472315 n.470T>C non_coding_transcript_exon_variant 0.18 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474291 n.634_649delTTTCCTCTCCGGAGGAinsC non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1474308 n.651G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474716 n.1059A>C non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1475006 n.1349A>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475007 n.1350C>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475013 n.1356G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1475018 n.1361G>T non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475019 n.1362T>A non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1475028 n.1371G>A non_coding_transcript_exon_variant 0.17 capreomycin
linezolid
rrl 1475061 n.1404C>A non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1475062 n.1405A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.26 capreomycin
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.22 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 0.26 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1475599 n.1942A>G non_coding_transcript_exon_variant 0.2 capreomycin
linezolid Uncertain significance
rrl 1475604 n.1947A>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475606 n.1949T>C non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
rrl 1475619 n.1962C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475622 n.1965G>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1475629 n.1972G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475635 n.1978G>A non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1475637 n.1980T>G non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674480 c.279T>C synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674486 c.285T>C synonymous_variant 0.15 ethionamide
isoniazid
inhA 1674489 c.288G>A synonymous_variant 0.16 ethionamide
isoniazid
inhA 1674498 c.297G>C synonymous_variant 0.17 ethionamide
isoniazid
inhA 1674503 p.Thr101Ser missense_variant 0.19 ethionamide
isoniazid
inhA 1674542 p.Ala114Glu missense_variant 0.16 ethionamide
isoniazid
inhA 1674546 c.345T>C synonymous_variant 0.15 ethionamide
isoniazid
inhA 1674576 c.375T>C synonymous_variant 0.13 ethionamide
isoniazid
inhA 1674579 c.378G>C synonymous_variant 0.13 ethionamide
isoniazid
inhA 1674585 c.384T>C synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674589 p.Met130Leu missense_variant 0.14 ethionamide
isoniazid
inhA 1674594 c.393C>A synonymous_variant 0.13 ethionamide
isoniazid
inhA 1674597 c.396G>A synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674601 c.400C>T synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674604 c.403C>T synonymous_variant 0.14 ethionamide
isoniazid
inhA 1674618 c.417C>T synonymous_variant 0.13 ethionamide
isoniazid
rpsA 1833664 c.123C>A synonymous_variant 0.12 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.18 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.23 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.2 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.19 pyrazinamide
rpsA 1833820 c.279G>A synonymous_variant 0.18 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.13 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.13 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.13 pyrazinamide
rpsA 1834123 c.582C>G synonymous_variant 0.12 pyrazinamide
rpsA 1834468 c.927A>G synonymous_variant 0.12 pyrazinamide
rpsA 1834489 c.948T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.16 pyrazinamide
rpsA 1834513 c.972C>G synonymous_variant 0.21 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.23 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.26 pyrazinamide
rpsA 1834606 c.1065C>T synonymous_variant 0.17 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.17 pyrazinamide
rpsA 1834612 c.1071G>T synonymous_variant 0.17 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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518705 c.591T>C synonymous_variant 0.14 isoniazid
eis 2715620 c.-288C>T upstream_gene_variant 1.0 amikacin
kanamycin
Rv2477c 2782750 c.1293T>C synonymous_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783628 p.Ala139Ser missense_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783632 c.411C>G synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783659 p.Glu128Asp missense_variant 0.16 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
Rv2477c 2783665 c.378A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783683 c.360A>G synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2783700 p.Thr115Ser missense_variant 0.12 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
thyX 3067391 c.555G>C synonymous_variant 0.12 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623375 c.1536T>C synonymous_variant 0.15 bedaquiline
rifampicin
lpqB 3623380 p.Ala511Thr missense_variant 0.16 bedaquiline
rifampicin
lpqB 3623388 p.Thr508Asn missense_variant 0.19 bedaquiline
rifampicin
lpqB 3623393 c.1518A>C synonymous_variant 0.2 bedaquiline
rifampicin
lpqB 3623414 c.1497C>G synonymous_variant 0.18 bedaquiline
rifampicin
lpqB 3623417 c.1494A>C synonymous_variant 0.18 bedaquiline
rifampicin
lpqB 3623423 p.Ser496Tyr missense_variant 0.2 bedaquiline
rifampicin
lpqB 3623428 c.1483T>C synonymous_variant 0.21 bedaquiline
rifampicin
lpqB 3623441 c.1468_1470delTCCinsAG frameshift_variant&stop_gained 0.24 bedaquiline
rifampicin Uncertain significance
lpqB 3623444 c.1467T>A synonymous_variant 0.23 bedaquiline
rifampicin
lpqB 3623450 c.1461G>C synonymous_variant 0.27 bedaquiline
rifampicin
lpqB 3623456 c.1455T>C synonymous_variant 0.28 bedaquiline
rifampicin
lpqB 3623468 c.1443T>G synonymous_variant 0.31 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3623492 c.1419T>C synonymous_variant 0.35 bedaquiline
rifampicin
lpqB 3623498 c.1413C>G synonymous_variant 0.3 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3623510 c.1401C>T synonymous_variant 0.33 bedaquiline
rifampicin
lpqB 3623516 c.1395C>G synonymous_variant 0.29 bedaquiline
rifampicin
lpqB 3624371 c.540T>G synonymous_variant 0.16 bedaquiline
rifampicin
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3625630 c.-720C>G upstream_gene_variant 0.13 bedaquiline
rifampicin
lpqB 3625648 c.-738T>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3625656 c.958T>C synonymous_variant 0.17 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3625663 c.-753G>C upstream_gene_variant 0.22 bedaquiline
rifampicin
lpqB 3625687 c.-777G>C upstream_gene_variant 0.14 bedaquiline
rifampicin
lpqB 3625690 c.-780T>C upstream_gene_variant 0.14 bedaquiline
rifampicin
lpqB 3625726 c.-816G>A upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrB 3625729 c.885A>G synonymous_variant 0.17 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626744 c.-131G>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626750 c.-137T>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrA 3626759 c.591T>C synonymous_variant 0.17 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626774 c.574_576delAGGinsCC frameshift_variant&missense_variant 0.18 bedaquiline
rifampicin
mtrB 3626780 c.-167T>C upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrB 3626783 c.-170C>G upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrA 3626786 c.564A>G synonymous_variant 0.22 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626798 c.-185T>A upstream_gene_variant 0.24 bedaquiline
rifampicin
mtrB 3626804 c.-191A>C upstream_gene_variant 0.23 bedaquiline
rifampicin
mtrB 3626843 c.-230G>C upstream_gene_variant 0.23 bedaquiline
rifampicin
mtrA 3626846 c.504G>A synonymous_variant 0.23 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626849 c.-236C>T upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrB 3626858 c.-245A>G upstream_gene_variant 0.24 bedaquiline
rifampicin
mtrB 3626885 c.-272A>G upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrA 3626888 c.460_462delTTGinsCC frameshift_variant&missense_variant 0.17 bedaquiline
rifampicin
mtrB 3626891 c.-278G>C upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3626903 c.-290T>C upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrA 3626912 c.438T>C synonymous_variant 0.17 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626930 c.-317A>G upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3626954 c.-341C>G upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3626966 c.-353C>A upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626969 c.-356C>G upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626972 c.-359A>G upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626987 c.-374C>G upstream_gene_variant 0.23 bedaquiline
rifampicin
mtrB 3626992 c.-379C>T upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrB 3627011 c.-398T>G upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3627059 c.-446G>C upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrA 3627068 c.282T>C synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627071 c.-458G>C upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrA 3627080 c.270T>C synonymous_variant 0.12 bedaquiline
rifampicin Not assoc w R - Interim
fbiB 3641298 c.-237G>A upstream_gene_variant 1.0 clofazimine
pretomanid
delamanid
rpoA 3877803 c.705G>A synonymous_variant 0.16 rifampicin
rpoA 3877818 c.690A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877839 c.669G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoA 3877848 c.660C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoA 3877857 c.651G>A synonymous_variant 0.19 rifampicin
rpoA 3877872 c.636C>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877875 c.633T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877881 c.627G>C synonymous_variant 0.13 rifampicin
rpoA 3877900 p.Ser203Thr missense_variant 0.13 rifampicin
rpoA 3877905 c.603A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoA 3877909 p.Asn200Ser missense_variant 0.16 rifampicin
rpoA 3877920 c.588G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877962 c.546G>T synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877968 c.540C>G synonymous_variant 0.13 rifampicin
rpoA 3878283 p.Glu75Asp missense_variant 0.12 rifampicin Uncertain significance
clpC1 4038308 c.2395_2397delGTGinsAC frameshift_variant&missense_variant 0.2 pyrazinamide
clpC1 4038314 c.2391T>A synonymous_variant 0.18 pyrazinamide
clpC1 4038320 c.2385G>T synonymous_variant 0.21 pyrazinamide
clpC1 4038350 c.2355C>G synonymous_variant 0.22 pyrazinamide
clpC1 4038356 c.2349T>C synonymous_variant 0.19 pyrazinamide
clpC1 4038359 c.2346A>G synonymous_variant 0.18 pyrazinamide
clpC1 4038368 c.2337T>C synonymous_variant 0.19 pyrazinamide
clpC1 4038398 c.2307G>C synonymous_variant 0.18 pyrazinamide
clpC1 4038403 c.2302T>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4038419 c.2286T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038434 c.2271G>A synonymous_variant 0.18 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4038881 c.1824C>T synonymous_variant 0.14 pyrazinamide
clpC1 4038890 c.1815G>A synonymous_variant 0.14 pyrazinamide
clpC1 4038997 c.1708T>C synonymous_variant 0.19 pyrazinamide Not assoc w R - Interim
clpC1 4039022 c.1683A>G synonymous_variant 0.26 pyrazinamide
clpC1 4039067 c.1638G>T synonymous_variant 0.28 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.28 pyrazinamide Not assoc w R - Interim
clpC1 4039097 c.1608G>C synonymous_variant 0.3 pyrazinamide
clpC1 4039106 c.1599G>T synonymous_variant 0.26 pyrazinamide
clpC1 4039112 c.1593C>G synonymous_variant 0.26 pyrazinamide
clpC1 4039121 c.1584T>C synonymous_variant 0.24 pyrazinamide
clpC1 4039124 c.1581C>G synonymous_variant 0.25 pyrazinamide
clpC1 4039133 c.1572C>G synonymous_variant 0.22 pyrazinamide
clpC1 4039140 p.Glu522Val missense_variant 0.16 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.14 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.14 pyrazinamide
clpC1 4040654 c.51G>A synonymous_variant 0.19 pyrazinamide
clpC1 4040657 c.48T>G synonymous_variant 0.18 pyrazinamide Not assoc w R - Interim
glpK 4139177 c.579T>C synonymous_variant 0.13 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139183 c.573T>C synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139186 c.570G>T synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139189 c.567G>C synonymous_variant 0.18 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139195 c.561G>C synonymous_variant 0.2 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4240766 c.904C>A synonymous_variant 0.19 ethambutol
embC 4240780 c.918T>C synonymous_variant 0.19 ethambutol
embC 4240783 c.921G>C synonymous_variant 0.19 ethambutol
embC 4240789 c.927T>C synonymous_variant 0.17 ethambutol
embC 4240819 c.957A>G synonymous_variant 0.15 ethambutol
embC 4240831 c.969T>G synonymous_variant 0.13 ethambutol
embC 4241671 c.1809T>G synonymous_variant 0.14 ethambutol
embC 4241674 c.1812C>G synonymous_variant 0.15 ethambutol
embC 4241680 c.1818C>G synonymous_variant 0.13 ethambutol
embC 4241689 c.1827G>T synonymous_variant 0.15 ethambutol
embC 4241692 c.1830C>A synonymous_variant 0.14 ethambutol
embC 4241695 c.1833T>C synonymous_variant 0.14 ethambutol
embC 4241707 c.1845G>C synonymous_variant 0.12 ethambutol
embC 4241708 c.1846C>A synonymous_variant 0.12 ethambutol
embC 4241713 c.1851G>C synonymous_variant 0.12 ethambutol
embC 4241719 c.1857G>C synonymous_variant 0.12 ethambutol
embC 4241734 c.1872C>A synonymous_variant 0.14 ethambutol
embC 4241737 c.1875G>C synonymous_variant 0.14 ethambutol
embC 4241741 c.1879_1881delGTCinsCG frameshift_variant&missense_variant 0.12 ethambutol
embC 4241750 p.Leu630Met missense_variant 0.19 ethambutol
embC 4241756 p.Leu632Met missense_variant 0.2 ethambutol
embC 4241770 c.1908T>C synonymous_variant 0.19 ethambutol Not assoc w R - Interim
embC 4241791 c.1929G>C synonymous_variant 0.17 ethambutol
embC 4241794 c.1932C>G synonymous_variant 0.16 ethambutol
embC 4241797 c.1935C>T synonymous_variant 0.16 ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.94 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