TB-Profiler result

Run: ERR4816100
Summary

Run ID: ERR4816100

Sample name:

Date: 2024-10-04T14:48:43.067707

Number of reads: 2349731

Percentage reads mapped: 75.28

Median coverage: 51.0

Strain: lineage1.1.2;lineage4.1.2.1;lineage4.1.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1.3 Euro-American None 0.49
lineage1.1.2 Indo-Oceanic RD239 0.4
lineage4.1 Euro-American None 0.6
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.08
lineage1.1 Indo-Oceanic RD239 0.36
lineage4 Euro-American None 0.66
lineage1 Indo-Oceanic RD239 0.35
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
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
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 840 c.840G>A synonymous_variant 0.15 isoniazid
dnaA 846 c.846T>C synonymous_variant 0.17 isoniazid
dnaA 849 c.849A>G synonymous_variant 0.16 isoniazid
gyrB 6112 p.Met291Ile missense_variant 0.34 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.35 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 6670 c.-632G>C upstream_gene_variant 0.13 levofloxacin
moxifloxacin
gyrA 6676 c.-626T>G upstream_gene_variant 0.13 levofloxacin
moxifloxacin
gyrA 6730 c.-572A>G upstream_gene_variant 0.13 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7484 c.183T>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 7490 c.189C>G synonymous_variant 0.13 levofloxacin
moxifloxacin
gyrA 7496 c.195C>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7499 c.198G>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 7523 c.222C>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7526 c.225G>C synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7532 c.231T>G synonymous_variant 0.18 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7559 c.258G>A synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 7571 c.270G>C synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7574 c.273G>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8435 c.1134C>G synonymous_variant 0.35 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8452 p.Ala384Val missense_variant 0.32 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8897 c.1596T>C synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8915 c.1614A>G synonymous_variant 0.15 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8924 c.1623C>T synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 9122 c.1821C>A synonymous_variant 0.12 levofloxacin
moxifloxacin
gyrA 9143 c.1842T>C synonymous_variant 0.59 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9182 c.1881T>C synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9191 c.1890G>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.37 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.29 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.33 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575376 p.Ser10Leu missense_variant 0.32 isoniazid Uncertain significance
ethionamide Uncertain significance
ccsA 619507 c.-384A>G upstream_gene_variant 0.16 kanamycin
capreomycin
amikacin
ccsA 619528 c.-363C>G upstream_gene_variant 0.16 kanamycin
capreomycin
amikacin
ccsA 619531 c.-360T>C upstream_gene_variant 0.16 kanamycin
capreomycin
amikacin
ccsA 619535 c.-356_-354delCAAinsGCG upstream_gene_variant 0.17 kanamycin
capreomycin
amikacin
ccsA 619543 c.-348C>G upstream_gene_variant 0.17 kanamycin
capreomycin
amikacin
ccsA 619552 c.-339A>G upstream_gene_variant 0.16 kanamycin
capreomycin
amikacin
ccsA 619555 c.-336C>G upstream_gene_variant 0.16 kanamycin
capreomycin
amikacin
ccsA 619561 c.-330G>C upstream_gene_variant 0.17 kanamycin
capreomycin
amikacin
ccsA 619591 c.-300G>C upstream_gene_variant 0.21 kanamycin
capreomycin
amikacin
ccsA 620688 c.798G>C synonymous_variant 0.15 kanamycin
capreomycin
amikacin
Rv0565c 657269 p.Ser68Pro missense_variant 0.65 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.42 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.16 rifampicin Not assoc w R
nusG 734442 c.189G>A synonymous_variant 0.16 rifampicin
rpoB 760112 c.306T>C synonymous_variant 0.14 rifampicin
rpoB 760115 c.309C>T synonymous_variant 0.13 rifampicin Not assoc w R
rpoB 760118 c.312T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760130 p.Asp108Glu missense_variant 0.19 rifampicin Uncertain significance
rpoB 760184 c.378A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.18 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760283 c.477G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 760484 c.678A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760522 p.Ser239Asn missense_variant 0.14 rifampicin Uncertain significance
rpoB 760634 c.828T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760661 c.855A>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760674 c.868T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760679 c.873A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760683 c.877T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760887 p.Thr361Ala missense_variant 0.13 rifampicin
rpoB 760910 c.1104C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761021 c.1215G>C synonymous_variant 0.16 rifampicin
rpoB 761027 c.1221A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761036 c.1230G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 761037 c.1231T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761057 c.1251G>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761102 c.1296A>G synonymous_variant 0.29 rifampicin
rpoB 761129 c.1323G>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761133 c.1327T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.23 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 0.16 rifampicin
rpoB 761312 c.1506G>C synonymous_variant 0.19 rifampicin
rpoB 761327 c.1521A>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 761330 c.1524G>C synonymous_variant 0.16 rifampicin
rpoB 761360 c.1554T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761362 p.Ser519Thr missense_variant 0.23 rifampicin
rpoB 761373 p.Val523His missense_variant 0.19 rifampicin
rpoB 761537 c.1731C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761570 c.1764T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761612 c.1806G>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761615 c.1809A>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoB 761636 c.1830G>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.19 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762233 c.2427G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762920 c.3114C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762959 c.3153G>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 762989 c.3183G>A synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 762995 c.3189G>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.43 rifampicin Not assoc w R
rpoB 763040 c.3234C>G synonymous_variant 0.25 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 0.15 rifampicin Not assoc w R - Interim
rpoB 763088 c.3282C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763094 c.3288G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 763115 c.3309T>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 763127 c.3321G>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 763136 c.3330C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763142 c.-228C>G upstream_gene_variant 0.15 rifampicin
rpoC 763402 c.33C>G synonymous_variant 0.18 rifampicin
rpoC 763411 c.42T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763414 c.45T>C synonymous_variant 0.18 rifampicin
rpoC 763441 c.72C>T synonymous_variant 0.19 rifampicin
rpoC 763444 c.75T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763456 c.87A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 763660 c.291T>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763675 c.306C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763702 c.333C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 763717 c.348T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 763723 c.354G>C synonymous_variant 0.18 rifampicin
rpoC 763732 c.363C>G synonymous_variant 0.19 rifampicin
rpoC 763741 c.372C>T synonymous_variant 0.17 rifampicin
rpoC 763765 c.396T>C synonymous_variant 0.15 rifampicin
rpoC 763884 p.Ala172Val missense_variant 0.52 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.55 rifampicin Not assoc w R
rpoC 764405 c.1036A>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764428 c.1059G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764431 c.1062G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764458 c.1089G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 764461 c.1092A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764497 c.1128A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764506 c.1137C>T synonymous_variant 0.24 rifampicin
rpoC 764527 c.1158C>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764554 c.1185C>T synonymous_variant 0.24 rifampicin
rpoC 764566 c.1197C>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoC 764578 c.1209C>G synonymous_variant 0.2 rifampicin
rpoC 764593 c.1224C>T synonymous_variant 0.22 rifampicin
rpoC 764602 c.1233C>T synonymous_variant 0.13 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764635 c.1266C>T synonymous_variant 0.18 rifampicin
rpoC 764650 c.1281G>T synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764752 c.1383G>C synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoC 764764 c.1395T>C synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.14 rifampicin Not assoc w R
rpoC 764815 c.1446A>G synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764827 c.1458G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764858 c.1489T>C synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 764875 c.1506C>A synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 764888 c.1519T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764911 c.1542A>G synonymous_variant 0.14 rifampicin
rpoC 764932 c.1563C>A synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764948 c.1579T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764968 c.1599T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 0.61 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.31 rifampicin Not assoc w R
rpoC 765700 c.2331T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765937 c.2568T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766607 p.Ile1080Leu missense_variant 0.14 rifampicin
rpoC 766630 c.3261G>C synonymous_variant 0.15 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.62 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781276 c.-284A>C upstream_gene_variant 0.14 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781421 c.-139C>A upstream_gene_variant 0.55 streptomycin Uncertain significance
rpsL 781832 c.273T>C synonymous_variant 0.16 streptomycin
rpsL 781868 c.309T>C synonymous_variant 0.18 streptomycin
rpsL 781871 c.312G>C synonymous_variant 0.18 streptomycin
rpsL 781892 c.333A>G synonymous_variant 0.18 streptomycin
rpsL 781898 c.339A>T synonymous_variant 0.18 streptomycin
rpsL 781916 c.357T>C synonymous_variant 0.17 streptomycin
rplC 800357 c.-452C>A upstream_gene_variant 0.25 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.37 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303818 c.888C>G synonymous_variant 0.21 pretomanid
delamanid
clofazimine
fbiC 1303836 c.906G>C synonymous_variant 0.22 pretomanid
delamanid
clofazimine
fbiC 1303845 c.915C>G synonymous_variant 0.22 pretomanid
delamanid
clofazimine
fbiC 1303846 p.Phe306Val missense_variant 0.22 pretomanid
delamanid
clofazimine
fbiC 1303854 c.924T>C synonymous_variant 0.22 pretomanid
delamanid
clofazimine
fbiC 1303860 c.930A>C synonymous_variant 0.22 pretomanid
delamanid
clofazimine
fbiC 1304610 c.1680C>T synonymous_variant 0.54 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304958 c.2028T>G synonymous_variant 0.18 pretomanid
delamanid
clofazimine
embR 1417554 c.-207C>G upstream_gene_variant 0.19 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471925 n.80T>C non_coding_transcript_exon_variant 0.17 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1471934 n.89A>G non_coding_transcript_exon_variant 0.19 kanamycin
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472106 n.261G>A non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1472108 n.263C>T non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472113 n.268T>C non_coding_transcript_exon_variant 0.18 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.19 kanamycin Uncertain significance
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrl 1473660 n.3G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1473806 n.149C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475120 n.1463G>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid
rrl 1475505 n.1848G>A non_coding_transcript_exon_variant 0.33 capreomycin Uncertain significance
linezolid
rrl 1475526 n.1869C>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.32 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.27 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476608 n.2951C>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674589 p.Met130Leu missense_variant 0.13 isoniazid
ethionamide
inhA 1674660 c.459G>C synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674703 c.502T>C synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674708 c.507G>A synonymous_variant 0.16 isoniazid
ethionamide
inhA 1674718 c.517A>C synonymous_variant 0.17 isoniazid
ethionamide
rpsA 1833841 c.300C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.18 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.2 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.19 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.24 pyrazinamide
rpsA 1833979 c.438T>C synonymous_variant 0.16 pyrazinamide
rpsA 1834000 c.459G>C synonymous_variant 0.19 pyrazinamide
rpsA 1834021 c.480C>T synonymous_variant 0.15 pyrazinamide
rpsA 1834030 c.489C>G synonymous_variant 0.19 pyrazinamide
rpsA 1834074 p.Lys178Arg missense_variant 0.13 pyrazinamide
rpsA 1834451 c.910T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834498 c.957C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834528 c.987T>C synonymous_variant 0.18 pyrazinamide
tsnR 1853974 c.369C>T synonymous_variant 0.52 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.4 linezolid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 0.96 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 0.37 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.3 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.34 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.41 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.46 isoniazid
kasA 2518777 c.663C>T synonymous_variant 0.14 isoniazid
kasA 2518825 c.711T>C synonymous_variant 0.21 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.29 isoniazid
Rv2681 2996912 c.174C>T synonymous_variant 0.33 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.47 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
thyA 3074175 c.297A>G synonymous_variant 0.13 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 0.98 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.47 ethionamide Uncertain significance
lpqB 3624236 c.675C>A synonymous_variant 0.34 rifampicin Not assoc w R - Interim
bedaquiline
lpqB 3624486 p.Asp142Gly missense_variant 0.22 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3624660 p.Ala84Gly missense_variant 0.58 rifampicin Uncertain significance
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625569 c.1045T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3625572 p.Thr348Ser missense_variant 0.13 rifampicin
bedaquiline
lpqB 3625579 c.-669A>G upstream_gene_variant 0.14 rifampicin
bedaquiline
mtrB 3626704 c.-91C>T upstream_gene_variant 0.15 rifampicin
bedaquiline
mtrB 3626732 c.-119A>G upstream_gene_variant 0.14 rifampicin
bedaquiline
mtrA 3627068 c.282T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
bedaquiline
mtrA 3627098 c.252A>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627104 c.-491C>G upstream_gene_variant 0.19 rifampicin
bedaquiline
mtrA 3627119 c.231T>G synonymous_variant 0.22 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3627167 c.-554T>C upstream_gene_variant 0.14 rifampicin
bedaquiline
rpoA 3877743 c.765T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3877764 c.744C>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3877782 c.726T>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3877785 c.723C>A synonymous_variant 0.14 rifampicin
rpoA 3877818 c.690A>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoA 3878193 c.315T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878217 c.291A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878271 c.237T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3878725 c.-218A>G upstream_gene_variant 0.18 rifampicin
rpoA 3878736 c.-229A>G upstream_gene_variant 0.19 rifampicin
rpoA 3878737 c.-230G>C upstream_gene_variant 0.19 rifampicin
rpoA 3878742 c.-235G>A upstream_gene_variant 0.19 rifampicin
rpoA 3878746 c.-239A>G upstream_gene_variant 0.19 rifampicin Uncertain significance
rpoA 3878749 c.-242G>T upstream_gene_variant 0.18 rifampicin
rpoA 3878761 c.-254G>C upstream_gene_variant 0.2 rifampicin
rpoA 3878764 c.-257A>G upstream_gene_variant 0.2 rifampicin
rpoA 3878785 c.-278T>G upstream_gene_variant 0.15 rifampicin
rpoA 3878806 c.-299C>G upstream_gene_variant 0.13 rifampicin
rpoA 3879079 c.-572A>G upstream_gene_variant 0.16 rifampicin
rpoA 3879088 c.-581A>C upstream_gene_variant 0.16 rifampicin
clpC1 4038388 c.2317T>C synonymous_variant 0.13 pyrazinamide
clpC1 4038596 c.2109A>G synonymous_variant 0.2 pyrazinamide
clpC1 4038953 c.1752A>G synonymous_variant 0.15 pyrazinamide
clpC1 4038956 c.1749T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038965 c.1740T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038971 c.1734T>C synonymous_variant 0.14 pyrazinamide
clpC1 4038974 c.1731T>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4038989 c.1716T>C synonymous_variant 0.16 pyrazinamide
clpC1 4039064 c.1641C>T synonymous_variant 0.15 pyrazinamide
clpC1 4039274 c.1431G>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4039694 c.1011G>C synonymous_variant 0.17 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.18 pyrazinamide
clpC1 4039934 c.771G>C synonymous_variant 0.14 pyrazinamide
clpC1 4039943 c.762G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039946 c.759A>G synonymous_variant 0.16 pyrazinamide
clpC1 4039949 c.756G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.22 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.2 pyrazinamide
clpC1 4039964 c.741C>G synonymous_variant 0.18 pyrazinamide
clpC1 4039979 c.726C>G synonymous_variant 0.25 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.16 pyrazinamide
clpC1 4040093 c.612C>G synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4040105 c.600C>G synonymous_variant 0.15 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 0.27 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.4 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.14 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.44 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.39 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.69 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.43 ethambutol Not assoc w R
embA 4245137 c.1905T>C synonymous_variant 0.13 ethambutol
embA 4245149 c.1917C>G synonymous_variant 0.15 ethambutol
embA 4245182 c.1950T>C synonymous_variant 0.14 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.45 ethambutol Not assoc w R
embB 4247356 c.843C>T synonymous_variant 0.53 ethambutol Not assoc w R - Interim
embB 4247470 c.957T>C synonymous_variant 0.14 ethambutol
embB 4247491 c.978G>C synonymous_variant 0.14 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.38 ethambutol Not assoc w R
embB 4247893 c.1380C>T synonymous_variant 0.16 ethambutol
embB 4247899 p.Met462Ile missense_variant 0.17 ethambutol
embB 4247905 c.1392G>C synonymous_variant 0.16 ethambutol Not assoc w R - Interim
embB 4247940 p.Leu476Trp missense_variant 0.14 ethambutol
embB 4247945 c.1432T>C synonymous_variant 0.15 ethambutol
embB 4247951 p.Ser480Ala missense_variant 0.14 ethambutol
embB 4247956 c.1443G>C synonymous_variant 0.15 ethambutol Not assoc w R - Interim
aftB 4268683 p.Gly52Ser missense_variant 0.53 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.4 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.31 ethambutol Not assoc w R
whiB6 4338441 p.Tyr27* stop_gained 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338449 p.Ala25Pro missense_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338603 c.-82C>T upstream_gene_variant 0.24 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 0.98 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.28 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.26 streptomycin Not assoc w R