TB-Profiler result

Run: ERR4820335
Summary

Run ID: ERR4820335

Sample name:

Date: 2024-04-15T18:56:16.236283

Number of reads: 1995326

Percentage reads mapped: 80.5

Median coverage: 41.0

Strain: lineage4.1.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.1 Euro-American None 0.99
lineage4.1.2 Euro-American None 0.99
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.99
lineage4 Euro-American 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.888G>A 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 1472733 n.888G>A non_coding_transcript_exon_variant 0.78 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
gyrA 7141 c.-161T>C upstream_gene_variant 0.24 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7457 c.156T>C synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 7514 c.213C>G synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7523 c.222C>A synonymous_variant 0.23 levofloxacin
moxifloxacin
gyrA 7532 c.231T>C synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7541 c.240C>G synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7547 c.246C>T synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 8588 c.1287G>A synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 8603 c.1302A>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8619 c.1318T>C synonymous_variant 0.19 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8624 c.1323G>C synonymous_variant 0.21 levofloxacin
moxifloxacin
gyrA 8636 c.1335A>C synonymous_variant 0.21 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8642 c.1341A>G synonymous_variant 0.21 levofloxacin
moxifloxacin
gyrA 8810 c.1509A>G synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 8816 c.1515C>G synonymous_variant 0.2 levofloxacin
moxifloxacin
gyrA 8818 p.Ser506Asn missense_variant 0.2 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8828 c.1527T>C synonymous_variant 0.21 levofloxacin
moxifloxacin
gyrA 8829 c.1528T>C synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8852 c.1551T>C synonymous_variant 0.26 levofloxacin
moxifloxacin
gyrA 8867 c.1566A>G synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8870 c.1569G>C synonymous_variant 0.23 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8873 c.1572A>C synonymous_variant 0.23 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8891 c.1590G>A synonymous_variant 0.24 levofloxacin
moxifloxacin
gyrA 8897 c.1596T>C synonymous_variant 0.23 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8903 c.1602T>C synonymous_variant 0.24 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 8933 c.1632G>C synonymous_variant 0.19 levofloxacin
moxifloxacin
gyrA 9089 c.1788G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 9119 c.1818A>G synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 9122 c.1821C>A synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 9143 c.1842T>C synonymous_variant 0.16 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9153 p.Thr618Glu missense_variant 0.14 levofloxacin
moxifloxacin
gyrA 9158 c.1857C>T synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9161 c.1860C>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.91 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.96 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 575845 c.498C>T synonymous_variant 0.13 ethionamide
isoniazid Not assoc w R - Interim
mshA 575884 c.537G>C synonymous_variant 0.2 ethionamide
isoniazid
mshA 575887 c.540G>C synonymous_variant 0.21 ethionamide
isoniazid
mshA 575893 c.546C>G synonymous_variant 0.21 ethionamide
isoniazid
mshA 575896 c.549G>C synonymous_variant 0.2 ethionamide
isoniazid
mshA 575908 c.561A>G synonymous_variant 0.16 ethionamide
isoniazid
mshA 575917 p.Asp190Glu missense_variant 0.17 ethionamide
isoniazid
mshA 575920 c.573C>G synonymous_variant 0.16 ethionamide
isoniazid
mshA 575924 p.Gly193Ser missense_variant 0.16 ethionamide
isoniazid
Rv0565c 657269 p.Ser68Pro missense_variant 0.91 ethionamide Uncertain significance
hadA 732308 p.Val127Ile missense_variant 0.12 isoniazid
nusG 734421 c.168A>G synonymous_variant 0.15 rifampicin
nusG 734424 c.171G>A synonymous_variant 0.14 rifampicin
nusG 734442 c.189G>A synonymous_variant 0.17 rifampicin
nusG 734451 c.198G>C synonymous_variant 0.17 rifampicin
nusG 734457 c.204C>G synonymous_variant 0.17 rifampicin
nusG 734472 c.219T>C synonymous_variant 0.17 rifampicin
nusG 734475 c.222T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
nusG 734490 c.237C>T synonymous_variant 0.84 rifampicin Not assoc w R
rpoB 760112 c.306T>C synonymous_variant 0.14 rifampicin
rpoB 760115 c.309C>T synonymous_variant 0.86 rifampicin Not assoc w R
rpoB 760118 c.312T>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760130 p.Asp108Glu missense_variant 0.14 rifampicin Uncertain significance
rpoB 760139 c.333A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 760142 c.336C>G synonymous_variant 0.14 rifampicin
rpoB 760283 c.477G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760307 c.501T>C synonymous_variant 0.13 rifampicin
rpoB 760310 c.504G>C synonymous_variant 0.13 rifampicin
rpoB 760328 c.522G>C synonymous_variant 0.17 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.17 rifampicin
rpoB 760340 c.534G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760946 c.1140A>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 760982 c.1176G>C synonymous_variant 0.31 rifampicin Not assoc w R - Interim
rpoB 760985 c.1179G>C synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 760991 c.1185G>C synonymous_variant 0.23 rifampicin
rpoB 761189 c.1383T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 761207 c.1401C>T synonymous_variant 0.2 rifampicin
rpoB 761213 c.1407G>C synonymous_variant 0.25 rifampicin
rpoB 761219 c.1413G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 761249 c.1443A>G synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 761255 c.1449T>G synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 761261 c.1455G>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 761306 c.1500C>G synonymous_variant 0.17 rifampicin
rpoB 761312 c.1506G>C synonymous_variant 0.18 rifampicin
rpoB 761570 c.1764T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761573 c.1767C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoB 761579 c.1773G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 761588 c.1782C>T synonymous_variant 0.17 rifampicin
rpoB 761606 c.1800C>G synonymous_variant 0.18 rifampicin
rpoB 761885 c.2079T>C synonymous_variant 0.15 rifampicin
rpoB 761906 c.2100C>G synonymous_variant 0.14 rifampicin
rpoB 761909 c.2103T>C synonymous_variant 0.13 rifampicin
rpoB 761912 c.2106T>C synonymous_variant 0.14 rifampicin
rpoB 761915 p.Asp703Glu missense_variant 0.14 rifampicin
rpoB 761916 p.Asp704Asn missense_variant 0.15 rifampicin
rpoB 762008 c.2202C>T synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoB 762014 c.2208C>T synonymous_variant 0.37 rifampicin
rpoB 762017 c.2211A>G synonymous_variant 0.35 rifampicin Not assoc w R - Interim
rpoB 762053 c.2247T>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762062 c.2256T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 762065 c.2259T>C synonymous_variant 0.19 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 762167 c.2361T>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763013 c.-357C>G upstream_gene_variant 0.21 rifampicin
rpoC 763025 c.-345C>T upstream_gene_variant 0.2 rifampicin
rpoB 763085 c.3279C>G synonymous_variant 0.12 rifampicin Not assoc w R - Interim
rpoC 763486 c.117T>G synonymous_variant 0.2 rifampicin
rpoC 763528 c.159G>A synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 763546 c.177A>G synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 763594 c.225C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 763603 c.234C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 763636 c.267T>C synonymous_variant 0.18 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.97 rifampicin Not assoc w R
rpoC 765404 p.Leu679Val missense_variant 0.22 rifampicin
rpoC 765409 c.2040T>C synonymous_variant 0.21 rifampicin
rpoC 765421 c.2052C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 765499 c.2130C>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.15 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.15 rifampicin
rpoC 765559 c.2190G>C synonymous_variant 0.15 rifampicin
rpoC 765580 c.2211G>C synonymous_variant 0.21 rifampicin
rpoC 765967 c.2598C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>G synonymous_variant 0.18 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766021 c.2652G>C synonymous_variant 0.16 rifampicin
rpoC 766447 c.3078T>C synonymous_variant 0.16 rifampicin
rpoC 766462 c.3093G>C synonymous_variant 0.16 rifampicin
rpoC 766738 c.3369G>C synonymous_variant 0.14 rifampicin
rpoC 766765 c.3396A>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766801 c.3432C>G synonymous_variant 0.15 rifampicin
rpoC 766804 c.3435A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 766882 c.3513C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 766895 c.3526T>C synonymous_variant 0.19 rifampicin
rpoC 766900 c.3531T>C synonymous_variant 0.19 rifampicin
rpoC 766933 c.3564A>G synonymous_variant 0.21 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.16 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781276 c.-284A>C upstream_gene_variant 1.0 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781628 c.69T>C synonymous_variant 0.15 streptomycin Not assoc w R - Interim
rpsL 781631 c.72G>C synonymous_variant 0.15 streptomycin
rpsL 781649 c.90T>C synonymous_variant 0.15 streptomycin
rpsL 781655 c.96T>C synonymous_variant 0.15 streptomycin
rpsL 781808 c.249C>T synonymous_variant 0.14 streptomycin
rpsL 781811 c.252C>T synonymous_variant 0.2 streptomycin
rplC 800693 c.-116A>G upstream_gene_variant 0.16 linezolid
fbiC 1303846 p.Phe306Val missense_variant 0.14 clofazimine
pretomanid
delamanid
fbiC 1303854 c.924T>C synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fbiC 1304778 c.1848T>C synonymous_variant 0.15 clofazimine
pretomanid
delamanid
fbiC 1304784 c.1854T>C synonymous_variant 0.13 clofazimine
pretomanid
delamanid
fbiC 1304808 c.1878C>G synonymous_variant 0.19 clofazimine
pretomanid
delamanid
fbiC 1304811 c.1881C>G synonymous_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1304817 c.1887T>C synonymous_variant 0.26 clofazimine
pretomanid
delamanid
fbiC 1304883 p.Glu651Asp missense_variant 0.22 clofazimine
pretomanid
delamanid
fbiC 1304891 p.Ile654Thr missense_variant 0.2 clofazimine
pretomanid
delamanid
fbiC 1304893 p.Gly655Ser missense_variant 0.2 clofazimine
pretomanid
delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472537 n.692C>T non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472544 n.699C>A non_coding_transcript_exon_variant 0.91 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472545 n.700A>T non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472566 n.721G>A non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472571 n.726G>C non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472579 n.734G>C non_coding_transcript_exon_variant 0.9 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472580 n.735C>T non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472581 n.736A>T non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472598 n.753A>C non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472599 n.754G>T non_coding_transcript_exon_variant 0.93 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472616 n.771G>A non_coding_transcript_exon_variant 0.95 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.86 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.87 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472744 n.899A>G non_coding_transcript_exon_variant 0.82 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.83 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472790 n.945T>C non_coding_transcript_exon_variant 0.16 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.81 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.76 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472895 n.1050C>T non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.65 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.52 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>A non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.47 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473035 n.1190G>A non_coding_transcript_exon_variant 0.81 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473055 n.1210C>T non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473056 n.1211A>T non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Not assoc w R
rrs 1473066 n.1221A>G non_coding_transcript_exon_variant 0.75 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473088 n.1243A>G non_coding_transcript_exon_variant 0.64 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473121 n.1276T>C non_coding_transcript_exon_variant 0.58 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1473145 n.1300C>T non_coding_transcript_exon_variant 0.69 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.68 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1833554 p.Thr5Ala missense_variant 0.15 pyrazinamide Uncertain significance
rpsA 1833568 c.27G>C synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
rpsA 1833589 c.48A>T synonymous_variant 0.17 pyrazinamide
rpsA 1833595 c.54T>C synonymous_variant 0.16 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.2 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.17 pyrazinamide
rpsA 1833748 c.207C>G synonymous_variant 0.17 pyrazinamide
rpsA 1833787 c.246C>G synonymous_variant 0.2 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.14 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.15 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.2 pyrazinamide
rpsA 1834618 c.1077G>C synonymous_variant 0.18 pyrazinamide
rpsA 1834633 c.1092A>G synonymous_variant 0.17 pyrazinamide
rpsA 1834639 c.1098T>C 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 2518076 c.-39C>T upstream_gene_variant 1.0 isoniazid
kasA 2518480 c.366T>C synonymous_variant 0.16 isoniazid
kasA 2518483 c.369C>G synonymous_variant 0.15 isoniazid
kasA 2518504 c.390T>C synonymous_variant 0.18 isoniazid
kasA 2518506 p.Ala131Glu missense_variant 0.19 isoniazid
kasA 2518519 c.405G>C synonymous_variant 0.18 isoniazid
kasA 2518528 c.414C>G synonymous_variant 0.27 isoniazid
kasA 2518540 c.426T>C synonymous_variant 0.26 isoniazid
kasA 2518561 c.447T>C synonymous_variant 0.18 isoniazid
kasA 2518609 p.Met165Ile missense_variant 0.13 isoniazid
kasA 2518768 c.654C>T synonymous_variant 0.24 isoniazid
kasA 2518777 c.663C>T synonymous_variant 0.24 isoniazid
kasA 2518783 c.669T>C synonymous_variant 0.23 isoniazid
kasA 2518789 c.675G>C synonymous_variant 0.21 isoniazid
kasA 2518792 c.678C>A synonymous_variant 0.2 isoniazid
kasA 2518795 c.681C>G synonymous_variant 0.21 isoniazid
kasA 2518825 c.711T>C synonymous_variant 0.16 isoniazid
Rv2477c 2782936 c.1107G>T synonymous_variant 0.15 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782948 c.1095A>G synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2477c 2782957 c.1086A>G synonymous_variant 0.17 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
Rv2477c 2783700 p.Thr115Ser missense_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.59 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.26 capreomycin
thyX 3067391 c.555G>C synonymous_variant 0.13 para-aminosalicylic_acid
thyX 3067394 c.552G>C synonymous_variant 0.13 para-aminosalicylic_acid
thyX 3067691 p.Ile85Met missense_variant 0.14 para-aminosalicylic_acid
thyX 3067694 c.252G>C synonymous_variant 0.13 para-aminosalicylic_acid
thyX 3067718 c.228C>G synonymous_variant 0.16 para-aminosalicylic_acid
thyX 3067721 c.225T>C synonymous_variant 0.14 para-aminosalicylic_acid
thyX 3067850 c.96A>C synonymous_variant 0.2 para-aminosalicylic_acid
thyX 3067869 p.Thr26Ser missense_variant 0.23 para-aminosalicylic_acid
thyX 3067874 c.72C>G synonymous_variant 0.22 para-aminosalicylic_acid
thyX 3067883 c.63C>G synonymous_variant 0.23 para-aminosalicylic_acid
thyX 3067886 c.60A>C synonymous_variant 0.21 para-aminosalicylic_acid
thyX 3067889 c.57C>G synonymous_variant 0.22 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3624707 c.204G>C synonymous_variant 0.19 bedaquiline
rifampicin
lpqB 3624722 c.189C>G synonymous_variant 0.19 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
lpqB 3624728 c.183C>T synonymous_variant 0.21 bedaquiline
rifampicin
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625572 p.Thr348Ser missense_variant 0.12 bedaquiline
rifampicin
lpqB 3625579 c.-669A>G upstream_gene_variant 0.14 bedaquiline
rifampicin
lpqB 3625612 c.-702G>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3625616 p.Arg333Ala missense_variant 0.15 bedaquiline
rifampicin
lpqB 3625624 c.-714C>G upstream_gene_variant 0.16 bedaquiline
rifampicin
mtrB 3625636 c.978C>G synonymous_variant 0.19 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625729 c.885A>G synonymous_variant 0.12 bedaquiline
rifampicin Not assoc w R - Interim
lpqB 3625735 c.-825C>T upstream_gene_variant 0.13 bedaquiline
rifampicin
lpqB 3625749 c.-839C>T upstream_gene_variant 0.14 bedaquiline
rifampicin
mtrB 3625750 c.864G>A synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3625755 p.Ala287Thr missense_variant 0.14 bedaquiline
rifampicin Uncertain significance
mtrB 3625765 c.849C>G synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626804 c.546A>G synonymous_variant 0.14 bedaquiline
rifampicin Not assoc w R - Interim
mtrA 3626939 c.411A>G synonymous_variant 0.15 bedaquiline
rifampicin Not assoc w R - Interim
mtrB 3626942 c.-329A>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3626957 c.-344G>C upstream_gene_variant 0.15 bedaquiline
rifampicin
mtrB 3626972 c.-359A>G upstream_gene_variant 0.15 bedaquiline
rifampicin
fbiA 3640612 p.Gly24Ser missense_variant 1.0 clofazimine
pretomanid
delamanid
rpoA 3877553 p.Glu319Gln missense_variant 0.15 rifampicin
rpoA 3877571 p.Pro313Ala missense_variant 0.17 rifampicin
rpoA 3877613 p.Ile299Val missense_variant 0.14 rifampicin
rpoA 3877679 p.Ala277Ser missense_variant 0.16 rifampicin
rpoA 3877686 c.822A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877692 c.816G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877704 c.804G>C synonymous_variant 0.15 rifampicin
rpoA 3878938 c.-431T>A upstream_gene_variant 0.17 rifampicin
ddn 3987001 p.Gly53Asp missense_variant 1.0 delamanid Uncertain significance
pretomanid
glpK 4139165 c.591A>G synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139168 c.588T>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139177 c.579T>C synonymous_variant 0.17 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139183 c.573T>C synonymous_variant 0.16 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139186 c.570G>C synonymous_variant 0.17 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4139195 c.561G>T synonymous_variant 0.18 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4139198 c.558C>G synonymous_variant 0.16 ethambutol Not assoc w R - Interim
moxifloxacin
streptomycin Not assoc w R - Interim
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
glpK 4139207 c.549T>C synonymous_variant 0.14 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
embC 4239298 c.-565C>T upstream_gene_variant 0.98 ethambutol Not assoc w R
embC 4241146 c.1284C>G synonymous_variant 0.13 ethambutol
embC 4241158 c.1296T>C synonymous_variant 0.13 ethambutol
embC 4241161 c.1299C>G synonymous_variant 0.13 ethambutol Not assoc w R - Interim
embC 4241162 c.1300T>C synonymous_variant 0.13 ethambutol
embC 4241170 c.1308G>C synonymous_variant 0.15 ethambutol
embC 4241203 c.1341T>C synonymous_variant 0.15 ethambutol
embC 4241206 c.1344G>C synonymous_variant 0.15 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.85 ethambutol Not assoc w R
embA 4242820 c.-413G>C upstream_gene_variant 0.15 ethambutol
embA 4245083 c.1851A>C synonymous_variant 0.15 ethambutol
embA 4245089 c.1857G>C synonymous_variant 0.16 ethambutol
embA 4245092 c.1860C>G synonymous_variant 0.15 ethambutol
embA 4245101 c.1869G>C synonymous_variant 0.16 ethambutol
embB 4247539 c.1026T>C synonymous_variant 0.13 ethambutol
embB 4248097 c.1584C>G synonymous_variant 0.14 ethambutol
embB 4248130 c.1617G>C synonymous_variant 0.17 ethambutol
embB 4248133 c.1620C>G synonymous_variant 0.16 ethambutol
embB 4248139 c.1626C>G synonymous_variant 0.16 ethambutol
embB 4248142 c.1629T>C synonymous_variant 0.16 ethambutol
embB 4248143 c.1630T>C synonymous_variant 0.16 ethambutol
embB 4248157 c.1644A>G synonymous_variant 0.15 ethambutol Not assoc w R - Interim
embB 4248373 c.1860C>G synonymous_variant 0.14 ethambutol
embB 4248386 c.1873C>A synonymous_variant 0.15 ethambutol
embB 4248407 p.Leu632Val missense_variant 0.13 ethambutol
embB 4248457 c.1944T>C synonymous_variant 0.19 ethambutol
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