TB-Profiler result

Run: ERR11465711
Summary

Run ID: ERR11465711

Sample name:

Date: 2024-03-27T00:15:26.416434

Number of reads: 1961711

Percentage reads mapped: 98.9

Median coverage: 42.0

Strain: lineage1.2.2.1;lineage4.4.1.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2.1 Indo-Oceanic RD239 0.42
lineage1.2.2 Indo-Oceanic RD239 0.39
lineage4.4.1 Euro-American (S-type) None 0.63
lineage4 Euro-American None 0.6
lineage4.4.1.1 Euro-American None 0.61
lineage1 Indo-Oceanic RD239 0.38
lineage4.4 Euro-American None 0.63
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 0.17 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
dnaA 237 c.237G>A synonymous_variant 0.38 isoniazid Not assoc w R - Interim
gyrB 4971 c.-269A>G upstream_gene_variant 0.71 levofloxacin
moxifloxacin
gyrB 5075 c.-165C>T upstream_gene_variant 0.43 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.38 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6154 c.915C>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6160 c.921C>G synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrB 6346 c.1107C>T synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 6760 c.-542G>C upstream_gene_variant 0.17 levofloxacin
moxifloxacin
gyrB 6841 c.1602T>C synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6850 c.1611C>A synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6856 c.1617T>C synonymous_variant 0.2 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrB 6862 c.1623C>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 7595 c.294C>G synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 7601 c.300C>G synonymous_variant 0.11 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7619 c.318C>T synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 8452 p.Ala384Val missense_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9138 p.Gln613Glu missense_variant 0.58 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.42 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9345 c.2044A>C synonymous_variant 0.17 levofloxacin
moxifloxacin
Rv0010c 13298 p.Ile87Met missense_variant 0.58 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.45 isoniazid Not assoc w R
fgd1 491060 p.Met93Thr missense_variant 0.35 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.23 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620659 p.Arg257Cys missense_variant 0.33 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.38 ethionamide
hadA 731747 c.-183T>C upstream_gene_variant 0.15 isoniazid
hadA 731753 c.-177A>G upstream_gene_variant 0.18 isoniazid
hadA 731774 c.-156T>C upstream_gene_variant 0.2 isoniazid
hadA 731789 c.-141A>G upstream_gene_variant 0.17 isoniazid
hadA 731860 c.-70C>G upstream_gene_variant 0.13 isoniazid
nusG 734116 c.-138T>C upstream_gene_variant 0.39 rifampicin Not assoc w R
nusG 734439 c.186C>G synonymous_variant 0.16 rifampicin
nusG 734442 c.189G>A synonymous_variant 0.16 rifampicin
nusG 734451 c.198G>C synonymous_variant 0.18 rifampicin
nusG 734454 c.201A>G synonymous_variant 0.18 rifampicin
nusG 734460 c.207G>C synonymous_variant 0.17 rifampicin
nusG 734505 c.252G>C synonymous_variant 0.13 rifampicin
nusG 734532 c.279A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
nusG 734541 c.288A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
nusG 734556 c.303C>T synonymous_variant 0.16 rifampicin
nusG 734559 c.306T>C synonymous_variant 0.16 rifampicin
nusG 734589 c.336G>C synonymous_variant 0.11 rifampicin
nusG 734610 c.357C>G synonymous_variant 0.13 rifampicin
rpoB 760091 c.285G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760101 c.295T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760112 c.306T>C synonymous_variant 0.23 rifampicin
rpoB 760118 c.312T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760130 p.Asp108Glu missense_variant 0.15 rifampicin Uncertain significance
rpoB 760139 c.333A>C synonymous_variant 0.12 rifampicin
rpoB 760142 c.336C>G synonymous_variant 0.12 rifampicin
rpoB 760184 c.378A>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 760328 c.522G>C synonymous_variant 0.14 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.15 rifampicin
rpoB 760337 c.531C>G synonymous_variant 0.15 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760424 c.618C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760457 c.651C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760463 c.657C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760475 c.669A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760481 c.675G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760487 c.681G>C synonymous_variant 0.16 rifampicin
rpoB 760508 c.702G>C synonymous_variant 0.18 rifampicin
rpoB 760511 c.705G>C synonymous_variant 0.17 rifampicin
rpoB 760522 p.Ser239Asn missense_variant 0.15 rifampicin Uncertain significance
rpoB 760591 p.Val262Ala missense_variant 0.13 rifampicin
rpoB 760611 c.805T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760928 c.1122G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760931 c.1125C>G synonymous_variant 0.19 rifampicin
rpoB 760946 c.1140A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 761015 c.1209G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 761234 c.1428G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 762083 c.2277T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762086 c.2280G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762101 c.2295C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762131 c.2325C>G synonymous_variant 0.18 rifampicin
rpoB 762134 c.2328C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 762143 c.2337T>C synonymous_variant 0.14 rifampicin
rpoB 762149 c.2343G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 762185 c.2379G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762329 c.2523G>C synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoB 762338 c.2532T>C synonymous_variant 0.11 rifampicin
rpoB 762347 c.2541T>C synonymous_variant 0.12 rifampicin
rpoC 762434 c.-936T>C upstream_gene_variant 0.12 rifampicin
rpoB 762470 c.2664G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.63 rifampicin Not assoc w R
rpoB 763094 c.3288G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763100 c.-270G>A upstream_gene_variant 0.18 rifampicin
rpoB 763115 c.3309T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 763127 c.3321G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763430 c.61_63delAGGinsCT frameshift_variant&missense_variant 0.14 rifampicin
rpoC 763435 c.66A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763444 c.75T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 763468 c.99G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763492 c.123G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 763747 c.378G>A synonymous_variant 0.16 rifampicin
rpoC 763884 p.Ala172Val missense_variant 0.34 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.35 rifampicin Not assoc w R
rpoC 764575 c.1206T>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764581 c.1212T>C synonymous_variant 0.21 rifampicin
rpoC 764746 c.1377G>A synonymous_variant 0.13 rifampicin
rpoC 764752 c.1383G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764758 c.1389C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764791 c.1422C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>G synonymous_variant 0.16 rifampicin
rpoC 764878 c.1509C>T synonymous_variant 0.16 rifampicin
rpoC 764888 c.1519T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.13 rifampicin
rpoC 764953 c.1584G>C synonymous_variant 0.13 rifampicin
rpoC 766426 c.3057C>T synonymous_variant 0.14 rifampicin
rpoC 766429 c.3060C>G synonymous_variant 0.14 rifampicin
rpoC 766801 c.3432C>G synonymous_variant 0.12 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.15 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.13 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.25 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>A synonymous_variant 0.23 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 0.4 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 777122 c.1359C>T synonymous_variant 0.15 clofazimine
bedaquiline
mmpL5 777128 c.1353A>G synonymous_variant 0.15 clofazimine
bedaquiline
mmpL5 777416 c.1065G>T synonymous_variant 0.69 clofazimine Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.46 linezolid Not assoc w R
rplC 800516 c.-293G>C upstream_gene_variant 0.18 linezolid
rplC 800537 c.-272C>T upstream_gene_variant 0.15 linezolid
rplC 800546 c.-263T>G upstream_gene_variant 0.15 linezolid
rplC 800865 c.57A>G synonymous_variant 0.15 linezolid
rplC 800867 p.Ser20Asn missense_variant 0.15 linezolid
rplC 800899 p.Ala31Thr missense_variant 0.37 linezolid Uncertain significance
rplC 801423 c.615G>C synonymous_variant 0.12 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.45 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364847 c.435G>C synonymous_variant 0.17 pyrazinamide
embR 1416628 c.720C>T synonymous_variant 0.54 ethambutol
embR 1417019 p.Cys110Tyr missense_variant 0.38 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.34 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.34 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1471842 n.-4T>G upstream_gene_variant 0.44 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472225 n.380C>A non_coding_transcript_exon_variant 0.22 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Uncertain significance
rrs 1472300 n.455C>T non_coding_transcript_exon_variant 0.25 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472489 n.644A>T non_coding_transcript_exon_variant 0.38 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTT non_coding_transcript_exon_variant 0.15 streptomycin
kanamycin
capreomycin
amikacin
rrs 1473290 n.1445delCinsTT non_coding_transcript_exon_variant 0.29 streptomycin
kanamycin
capreomycin
amikacin
rrl 1473876 n.219G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473899 n.242A>T non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474139 n.482C>T non_coding_transcript_exon_variant 0.22 capreomycin
linezolid
rrl 1474140 n.483C>T non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474151 n.494C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474181 n.524C>T non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid
rrl 1474266 n.609T>C non_coding_transcript_exon_variant 0.27 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 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474310 n.653T>G non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474412 n.756_768delACCCACACGCGCA non_coding_transcript_exon_variant 0.16 capreomycin
linezolid
rrl 1474428 n.771C>T non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474429 n.772G>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474431 n.774G>C non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474434 n.777_778insAAGGG non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474437 n.781_782delAA non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1474447 n.790G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474716 n.1059A>C non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1474794 n.1137C>A non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474831 n.1174A>G non_coding_transcript_exon_variant 0.31 capreomycin Uncertain significance
linezolid
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475402 n.1745C>T non_coding_transcript_exon_variant 0.25 capreomycin
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475479 n.1822C>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475480 n.1823A>T non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475573 n.1916G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1475760 n.2103C>T non_coding_transcript_exon_variant 0.27 capreomycin
linezolid
rrl 1475763 n.2106C>T non_coding_transcript_exon_variant 0.28 capreomycin Uncertain significance
linezolid
rrl 1475975 n.2318C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475977 n.2320A>G non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476580 n.2923G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid
rrl 1476619 n.2962C>T non_coding_transcript_exon_variant 0.15 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674117 c.-85C>G upstream_gene_variant 0.13 ethionamide
isoniazid
inhA 1674703 c.502T>C synonymous_variant 0.19 ethionamide
isoniazid
inhA 1674718 c.517A>C synonymous_variant 0.19 ethionamide
isoniazid
rpsA 1833661 c.120A>G synonymous_variant 0.25 pyrazinamide
rpsA 1833664 c.123C>A synonymous_variant 0.23 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.21 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.22 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.22 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.23 pyrazinamide
rpsA 1833802 c.261A>G synonymous_variant 0.31 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.24 pyrazinamide
rpsA 1833820 c.279G>A synonymous_variant 0.3 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.28 pyrazinamide
rpsA 1833859 c.318C>T synonymous_variant 0.28 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.26 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.19 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.18 pyrazinamide
rpsA 1833976 c.435C>T synonymous_variant 0.16 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834012 c.471G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834015 c.474G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.14 pyrazinamide
rpsA 1834051 c.510G>A synonymous_variant 0.15 pyrazinamide
rpsA 1834093 c.552G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834102 c.561T>G synonymous_variant 0.17 pyrazinamide
rpsA 1834186 c.645C>G synonymous_variant 0.15 pyrazinamide
rpsA 1834189 c.648G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.18 pyrazinamide
rpsA 1834546 c.1005T>C synonymous_variant 0.25 pyrazinamide
rpsA 1834600 c.1059G>C synonymous_variant 0.17 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.12 pyrazinamide
rpsA 1834654 p.Glu371Asp missense_variant 0.19 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 0.4 linezolid Not assoc w R
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 2062922 p.Ile603Val missense_variant 0.53 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102990 p.Val18Ala missense_variant 0.6 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.47 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.38 pyrazinamide Not assoc w R
PPE35 2168479 p.Thr712Pro missense_variant 0.47 pyrazinamide Not assoc w R
PPE35 2169840 p.Gly258Asp missense_variant 0.57 pyrazinamide Not assoc w R
PPE35 2169902 c.711G>C synonymous_variant 0.13 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.35 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2517941 c.-174C>G upstream_gene_variant 0.15 isoniazid
kasA 2517950 c.-165C>G upstream_gene_variant 0.21 isoniazid
kasA 2517989 c.-126T>C upstream_gene_variant 0.13 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.49 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.41 isoniazid
ahpC 2726390 c.198G>C synonymous_variant 0.12 isoniazid
ahpC 2726393 c.201G>C synonymous_variant 0.12 isoniazid
thyX 3067570 p.Ala126Pro missense_variant 0.19 para-aminosalicylic_acid
thyX 3067721 c.225T>C synonymous_variant 0.18 para-aminosalicylic_acid
thyX 3067727 c.219A>C synonymous_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448608 c.105G>A synonymous_variant 0.74 ethionamide Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.35 ethionamide Uncertain significance
whiB7 3568779 c.-100T>C upstream_gene_variant 0.49 streptomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
Rv3236c 3612665 p.Val151Ala missense_variant 0.65 pyrazinamide Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.47 bedaquiline Uncertain significance
rifampicin Not assoc w R
lpqB 3624734 c.177A>C synonymous_variant 0.14 bedaquiline
rifampicin
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625222 c.1392T>C synonymous_variant 0.29 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625240 c.-330T>C upstream_gene_variant 0.3 bedaquiline
rifampicin
lpqB 3625243 c.-333T>C upstream_gene_variant 0.33 bedaquiline
rifampicin
lpqB 3625246 c.-336G>A upstream_gene_variant 0.35 bedaquiline
rifampicin
lpqB 3625255 c.-345T>C upstream_gene_variant 0.33 bedaquiline
rifampicin
lpqB 3625258 c.-348G>C upstream_gene_variant 0.32 bedaquiline
rifampicin
mtrB 3625267 c.1347T>C synonymous_variant 0.36 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625270 c.-360G>C upstream_gene_variant 0.36 bedaquiline
rifampicin
lpqB 3625282 c.-372C>G upstream_gene_variant 0.3 bedaquiline
rifampicin
lpqB 3625285 c.-375G>C upstream_gene_variant 0.35 bedaquiline
rifampicin
lpqB 3625291 c.-381A>G upstream_gene_variant 0.29 bedaquiline
rifampicin
mtrB 3625321 c.1293A>G synonymous_variant 0.2 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3625327 c.-417A>G upstream_gene_variant 0.18 bedaquiline
rifampicin
lpqB 3625483 c.-573C>G upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3625489 c.1123_1125delACAinsTC frameshift_variant&missense_variant 0.14 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrB 3625656 c.958T>C synonymous_variant 0.22 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3625663 c.-753G>C upstream_gene_variant 0.24 bedaquiline
rifampicin
lpqB 3625687 c.-777G>C upstream_gene_variant 0.29 bedaquiline
rifampicin
lpqB 3625690 c.-780T>G upstream_gene_variant 0.29 bedaquiline
rifampicin
lpqB 3625726 c.-816G>A upstream_gene_variant 0.23 bedaquiline
rifampicin
mtrB 3625729 c.885A>G synonymous_variant 0.23 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625747 c.867G>C synonymous_variant 0.22 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625755 p.Ala287Thr missense_variant 0.2 bedaquiline
rifampicin Uncertain significance
mtrB 3625762 c.852A>G synonymous_variant 0.2 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625786 c.-876C>T upstream_gene_variant 0.2 bedaquiline
rifampicin
lpqB 3625864 c.-954T>G upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrB 3625867 c.747A>G synonymous_variant 0.17 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625897 c.-987G>C upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3626025 c.589C>T synonymous_variant 0.21 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3626095 p.Glu173Asp missense_variant 0.16 bedaquiline
rifampicin
mtrB 3626101 p.Gln171His missense_variant 0.17 bedaquiline
rifampicin
mtrB 3626110 c.504C>G synonymous_variant 0.17 bedaquiline
rifampicin
mtrB 3626125 c.489C>T synonymous_variant 0.13 bedaquiline
rifampicin
mtrB 3626131 c.483G>C synonymous_variant 0.14 bedaquiline
rifampicin
mtrB 3626137 c.477G>A synonymous_variant 0.15 bedaquiline
rifampicin
mtrB 3626344 c.270G>C synonymous_variant 0.2 bedaquiline
rifampicin
mtrB 3626357 p.Thr86Asn missense_variant 0.21 bedaquiline
rifampicin
mtrB 3626362 c.252A>G synonymous_variant 0.23 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626437 c.177T>C synonymous_variant 0.17 bedaquiline
rifampicin
mtrB 3626440 c.174C>T synonymous_variant 0.17 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3626443 c.171T>G synonymous_variant 0.17 bedaquiline
rifampicin
mtrB 3626452 c.162C>T synonymous_variant 0.16 bedaquiline
rifampicin
mtrB 3626711 c.-98T>C upstream_gene_variant 0.13 bedaquiline
rifampicin
mtrA 3626723 c.627C>T synonymous_variant 0.25 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626744 c.-131G>C upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrB 3626750 c.-137T>C upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrA 3626759 c.591T>C synonymous_variant 0.25 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626774 c.574_576delAGGinsCT frameshift_variant&missense_variant 0.15 bedaquiline
rifampicin
mtrB 3626780 c.-167T>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3626783 c.-170C>G upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrA 3626786 c.564A>G synonymous_variant 0.15 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626798 c.-185T>C upstream_gene_variant 0.25 bedaquiline
rifampicin
mtrB 3626804 c.-191A>C upstream_gene_variant 0.22 bedaquiline
rifampicin
mtrB 3626843 c.-230G>C upstream_gene_variant 0.19 bedaquiline
rifampicin
mtrA 3626846 c.504G>A synonymous_variant 0.19 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626849 c.-236C>T upstream_gene_variant 0.2 bedaquiline
rifampicin
mtrB 3626858 c.-245A>G upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3626866 c.-253T>C upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrB 3626885 c.-272A>G upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrB 3626890 c.-277T>C upstream_gene_variant 0.23 bedaquiline
rifampicin
mtrA 3626912 c.438T>C synonymous_variant 0.26 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626930 c.-317A>G upstream_gene_variant 0.31 bedaquiline
rifampicin
mtrA 3626939 p.Glu137Asp missense_variant 0.45 bedaquiline
rifampicin
mtrB 3626942 c.-329A>C upstream_gene_variant 0.44 bedaquiline
rifampicin
mtrB 3626969 c.-356C>G upstream_gene_variant 0.3 bedaquiline
rifampicin
mtrB 3626972 c.-359A>G upstream_gene_variant 0.3 bedaquiline
rifampicin
mtrB 3626993 c.-380G>C upstream_gene_variant 0.26 bedaquiline
rifampicin
mtrB 3627011 c.-398T>C upstream_gene_variant 0.25 bedaquiline
rifampicin
mtrB 3627059 c.-446G>C upstream_gene_variant 0.21 bedaquiline
rifampicin
mtrA 3627068 c.282T>C synonymous_variant 0.22 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627071 c.-458G>C upstream_gene_variant 0.23 bedaquiline
rifampicin
mtrA 3627080 c.270T>C synonymous_variant 0.23 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3627098 c.252A>C synonymous_variant 0.16 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3627104 c.-491C>G upstream_gene_variant 0.17 bedaquiline
rifampicin
mtrB 3627110 c.-497G>C upstream_gene_variant 0.18 bedaquiline
rifampicin
mtrB 3627119 c.-506T>C upstream_gene_variant 0.12 bedaquiline
rifampicin
mtrB 3627122 c.-509T>C upstream_gene_variant 0.12 bedaquiline
rifampicin
mtrB 3627125 c.-512C>G upstream_gene_variant 0.12 bedaquiline
rifampicin
mtrB 3627139 c.-526T>C upstream_gene_variant 0.13 bedaquiline
rifampicin
alr 3841546 c.-126C>A upstream_gene_variant 0.17 cycloserine
clpC1 4038575 c.2130C>G synonymous_variant 0.13 pyrazinamide
clpC1 4038596 c.2109A>G synonymous_variant 0.17 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.19 pyrazinamide
clpC1 4038645 p.Glu687Ala missense_variant 0.16 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.12 pyrazinamide
clpC1 4038838 c.1867C>T synonymous_variant 0.18 pyrazinamide
clpC1 4038878 c.1827A>G synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038881 c.1824C>T synonymous_variant 0.17 pyrazinamide
clpC1 4038908 c.1797C>G synonymous_variant 0.12 pyrazinamide
clpC1 4038914 c.1791G>C synonymous_variant 0.12 pyrazinamide
clpC1 4038923 c.1782A>G synonymous_variant 0.12 pyrazinamide
clpC1 4038941 c.1764G>C synonymous_variant 0.13 pyrazinamide
clpC1 4039298 c.1407T>C synonymous_variant 0.13 pyrazinamide
clpC1 4039355 c.1350G>C synonymous_variant 0.12 pyrazinamide
clpC1 4039430 c.1275T>C synonymous_variant 0.14 pyrazinamide
clpC1 4040177 c.528C>T synonymous_variant 0.13 pyrazinamide
clpC1 4040369 c.336C>G synonymous_variant 0.13 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.43 pyrazinamide Not assoc w R - Interim
clpC1 4040644 c.61A>C synonymous_variant 0.15 pyrazinamide
clpC1 4040654 c.51G>A synonymous_variant 0.23 pyrazinamide
clpC1 4040657 c.48T>G synonymous_variant 0.24 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.37 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4139987 c.-232G>A upstream_gene_variant 0.51 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4238963 c.-900C>T upstream_gene_variant 0.68 ethambutol Not assoc w R
embC 4240519 c.657T>C synonymous_variant 0.13 ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.47 ethambutol Not assoc w R
embC 4240750 c.888C>T synonymous_variant 0.51 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.41 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4244666 c.1434G>C synonymous_variant 0.26 ethambutol
embA 4244668 p.Val479Ala missense_variant 0.26 ethambutol
embA 4244675 c.1443A>G synonymous_variant 0.29 ethambutol
embA 4244681 c.1449A>G synonymous_variant 0.27 ethambutol Not assoc w R - Interim
embA 4244684 c.1452C>T synonymous_variant 0.27 ethambutol
embA 4244695 p.Lys488Thr missense_variant 0.36 ethambutol
embA 4244702 c.1470C>G synonymous_variant 0.35 ethambutol
embA 4245321 p.Met697Val missense_variant 0.41 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.42 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.62 ethambutol Not assoc w R
aftB 4267517 c.1320A>G synonymous_variant 0.33 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 0.33 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.36 ethambutol Not assoc w R
ethA 4326439 p.Asn345Lys missense_variant 0.5 ethionamide Uncertain significance
ethA 4327450 c.24C>T synonymous_variant 0.33 ethionamide Not assoc w R - Interim
whiB6 4338545 c.-24G>A upstream_gene_variant 0.43 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 4338600 c.-79T>C upstream_gene_variant 0.4 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338603 c.-82C>T upstream_gene_variant 0.41 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338621 c.-100G>T upstream_gene_variant 0.41 capreomycin
amikacin
kanamycin
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.37 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.51 streptomycin Not assoc w R
gid 4408082 p.Val41Leu missense_variant 0.45 streptomycin Uncertain significance