TB-Profiler result

Run: ERR4797285
Summary

Run ID: ERR4797285

Sample name:

Date: 2024-10-05T12:37:50.508474

Number of reads: 3495294

Percentage reads mapped: 87.7

Median coverage: 105.0

Strain: lineage1.2.2.2

Spoligotype:

Drug-resistance: MDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.98
lineage1.2.2.2 Indo-Oceanic RD239 0.99
lineage1 Indo-Oceanic RD239 0.96
lineage6.2.1 West-Africa 2 RD702 0.07
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ser94Ala Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ethambutol embB p.Gly406Ala Assoc w R
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-770T>C Assoc w R - Interim Alias fabG1_c.-8T>C
p.Ser94Ala Assoc w R - Interim
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
rpoB 761155 p.Ser450Leu missense_variant 0.89 rifampicin Assoc w R
inhA 1673432 c.-770T>C upstream_gene_variant 1.0 ethionamide Assoc w R - Interim Alias fabG1_c.-8T>C
isoniazid Assoc w R - Interim Alias fabG1_c.-8T>C. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1674481 p.Ser94Ala missense_variant 0.82 ethionamide Assoc w R - Interim
isoniazid Assoc w R - Interim Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol Assoc w R
Non-Associated Mutations: This table reports mutations found in candidate resistance genes which have not been associated with drug resistance
Gene Chromosome position Mutation Type Estimated fraction Drugs Confidence
gyrB 5075 c.-165C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8452 p.Ala384Val missense_variant 0.9 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 1.0 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 9626 c.2325T>C synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 9630 p.Val777Ile missense_variant 0.15 levofloxacin
moxifloxacin
gyrA 9635 c.2334T>C synonymous_variant 0.15 levofloxacin
moxifloxacin
gyrA 9641 c.2340C>G synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 9644 c.2343T>C synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 9650 c.2349G>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 9656 c.2355C>G synonymous_variant 0.17 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9665 c.2364A>T synonymous_variant 0.17 levofloxacin
moxifloxacin
gyrA 9674 c.2373T>C synonymous_variant 0.16 levofloxacin
moxifloxacin
gyrA 9686 c.2385A>G synonymous_variant 0.14 levofloxacin
moxifloxacin
gyrA 9698 c.2397G>A synonymous_variant 0.14 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
Rv0010c 13298 p.Ile87Met missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 1.0 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 1.0 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide
Rv0565c 657734 c.-264T>C upstream_gene_variant 0.14 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.96 rifampicin Not assoc w R
rpoB 760193 c.387C>G synonymous_variant 0.15 rifampicin
rpoB 760196 c.390C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760223 c.417T>C synonymous_variant 0.17 rifampicin
rpoB 760235 c.429T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760283 c.477G>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoB 760307 c.501T>G synonymous_variant 0.15 rifampicin
rpoB 760310 c.504G>C synonymous_variant 0.15 rifampicin
rpoB 760313 c.507G>C synonymous_variant 0.15 rifampicin
rpoB 760331 c.525G>C synonymous_variant 0.18 rifampicin
rpoB 760340 c.534G>C synonymous_variant 0.19 rifampicin
rpoB 760361 c.555T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoB 760376 p.Asp190Glu missense_variant 0.24 rifampicin Uncertain significance
rpoB 760406 c.600G>C synonymous_variant 0.25 rifampicin
rpoB 760418 c.612G>C synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoB 760424 c.618C>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoB 760430 c.624T>C synonymous_variant 0.18 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 760563 c.757C>A synonymous_variant 0.14 rifampicin
rpoB 760646 c.840C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoB 760718 c.912C>G synonymous_variant 0.19 rifampicin
rpoB 760721 c.915C>G synonymous_variant 0.16 rifampicin
rpoB 760724 c.918T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760730 c.924T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760757 c.951T>C synonymous_variant 0.16 rifampicin
rpoB 760759 p.Val318Ala missense_variant 0.16 rifampicin
rpoB 760763 c.957C>T synonymous_variant 0.14 rifampicin
rpoB 760769 c.963C>G synonymous_variant 0.14 rifampicin
rpoB 760775 c.969G>C synonymous_variant 0.14 rifampicin
rpoB 760776 c.970_972delTCGinsAGC synonymous_variant 0.15 rifampicin
rpoB 760805 c.999G>C synonymous_variant 0.15 rifampicin
rpoB 760817 c.1011A>G synonymous_variant 0.15 rifampicin
rpoB 760820 c.1014T>C synonymous_variant 0.16 rifampicin
rpoB 760830 c.1024T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoB 760841 c.1035T>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 760850 c.1044G>C synonymous_variant 0.16 rifampicin
rpoB 761606 c.1800C>G synonymous_variant 0.13 rifampicin
rpoB 761636 c.1830G>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761645 c.1839C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761648 c.1842T>C synonymous_variant 0.14 rifampicin
rpoB 761657 c.1851C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 761669 c.1863C>T synonymous_variant 0.17 rifampicin
rpoB 761675 c.1869G>C synonymous_variant 0.18 rifampicin
rpoB 761682 c.1876C>T synonymous_variant 0.19 rifampicin
rpoB 761687 c.1881C>T synonymous_variant 0.18 rifampicin
rpoB 761723 c.1917A>G synonymous_variant 0.16 rifampicin
rpoB 761726 c.1920A>G synonymous_variant 0.16 rifampicin
rpoB 761765 c.1959T>G synonymous_variant 0.14 rifampicin
rpoB 761768 c.1962G>C synonymous_variant 0.13 rifampicin
rpoB 762296 c.2490G>A synonymous_variant 0.14 rifampicin
rpoB 762314 c.2508C>T synonymous_variant 0.16 rifampicin
rpoB 762317 c.2511A>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762338 c.2532T>C synonymous_variant 0.17 rifampicin
rpoB 762347 c.2541T>C synonymous_variant 0.17 rifampicin
rpoB 762350 c.2544C>G synonymous_variant 0.15 rifampicin
rpoB 762353 c.2547C>G synonymous_variant 0.15 rifampicin
rpoB 762362 p.Glu852Asp missense_variant 0.14 rifampicin
rpoC 762434 c.-936T>C upstream_gene_variant 0.14 rifampicin
rpoB 762813 p.Met1003Val missense_variant 0.16 rifampicin
rpoB 762818 c.3012C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762894 c.3088C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 762902 c.-468C>T upstream_gene_variant 0.18 rifampicin
rpoB 762929 c.3123G>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoB 762962 c.3156C>T synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 762995 c.3189G>T synonymous_variant 0.26 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 0.76 rifampicin Not assoc w R
rpoB 763031 c.3225T>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoB 763034 c.3228C>G synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoB 763040 c.3234C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 763049 c.-321G>A upstream_gene_variant 0.15 rifampicin
rpoB 763053 c.3247T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoB 763070 c.3264T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763124 c.-246C>T upstream_gene_variant 0.14 rifampicin
rpoC 763687 c.318C>T synonymous_variant 0.14 rifampicin
rpoC 763717 c.348T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 763732 c.363C>G synonymous_variant 0.15 rifampicin
rpoC 763884 p.Ala172Val missense_variant 0.9 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.9 rifampicin Not assoc w R
rpoC 764188 c.819A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764194 p.Glu275Asp missense_variant 0.15 rifampicin
rpoC 764195 p.Ser276Ala missense_variant 0.16 rifampicin
rpoC 764209 c.840C>G synonymous_variant 0.13 rifampicin
rpoC 764221 c.852C>T synonymous_variant 0.14 rifampicin
rpoC 764269 c.900G>C synonymous_variant 0.15 rifampicin
rpoC 764272 c.903G>C synonymous_variant 0.15 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764284 c.915G>C synonymous_variant 0.14 rifampicin
rpoC 764506 c.1137C>T synonymous_variant 0.14 rifampicin
rpoC 764510 c.1141C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764521 c.1152T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 764560 c.1191T>C synonymous_variant 0.25 rifampicin Not assoc w R - Interim
rpoC 764566 c.1197C>G synonymous_variant 0.24 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>C synonymous_variant 0.23 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.22 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764893 c.1524T>C synonymous_variant 0.14 rifampicin
rpoC 765307 p.Ile646Met missense_variant 0.14 rifampicin
rpoC 765319 c.1950A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 765328 p.His653Gln missense_variant 0.18 rifampicin Uncertain significance
rpoC 765330 p.Ser654Asn missense_variant 0.17 rifampicin Uncertain significance
rpoC 765409 c.2040T>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoC 765421 c.2052C>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 765451 c.2082C>T synonymous_variant 0.23 rifampicin
rpoC 765478 c.2109T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765496 c.2127C>G synonymous_variant 0.16 rifampicin
rpoC 765499 c.2130C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.22 rifampicin
rpoC 765541 c.2172C>G synonymous_variant 0.2 rifampicin
rpoC 765547 c.2178C>A synonymous_variant 0.2 rifampicin
rpoC 765562 c.2193G>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 765565 c.2196G>C synonymous_variant 0.18 rifampicin
rpoC 765578 c.2209C>T synonymous_variant 0.15 rifampicin
rpoC 765583 c.2214G>C synonymous_variant 0.15 rifampicin
rpoC 765904 c.2535C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 765937 c.2568T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 765979 c.2610C>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765982 c.2613C>G synonymous_variant 0.15 rifampicin
rpoC 765985 c.2616C>T synonymous_variant 0.15 rifampicin
rpoC 765994 c.2625A>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766021 c.2652G>C synonymous_variant 0.15 rifampicin
rpoC 766522 c.3153C>T synonymous_variant 0.14 rifampicin
rpoC 766525 c.3156G>C synonymous_variant 0.14 rifampicin
rpoC 766528 c.3159T>C synonymous_variant 0.14 rifampicin
rpoC 766531 c.3162G>T synonymous_variant 0.14 rifampicin
rpoC 766543 c.3174C>T synonymous_variant 0.15 rifampicin
rpoC 766657 c.3288A>G synonymous_variant 0.16 rifampicin
rpoC 766672 c.3303T>C synonymous_variant 0.15 rifampicin
rpoC 766675 c.3306C>T synonymous_variant 0.16 rifampicin
rpoC 766684 c.3315C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 766738 c.3369G>C synonymous_variant 0.14 rifampicin
rpoC 766945 c.3576A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766996 c.3627C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 767002 c.3633G>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767030 c.3661C>T synonymous_variant 0.2 rifampicin
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.2 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.17 rifampicin
rpoC 767074 c.3705T>C synonymous_variant 0.16 rifampicin
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 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 777431 c.1047_1049delCGC disruptive_inframe_deletion 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 1.0 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
fbiC 1303797 c.867A>G synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fbiC 1303800 c.870G>C synonymous_variant 0.14 pretomanid
delamanid
clofazimine
fbiC 1304829 c.1899T>C synonymous_variant 0.21 pretomanid
delamanid
clofazimine
fbiC 1304832 c.1902C>G synonymous_variant 0.21 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
fbiC 1304853 c.1923C>A synonymous_variant 0.19 pretomanid
delamanid
clofazimine
fbiC 1304856 c.1926C>T synonymous_variant 0.18 pretomanid
delamanid
clofazimine
fbiC 1304868 c.1938G>C synonymous_variant 0.19 pretomanid
delamanid
clofazimine
fbiC 1304869 p.Leu647Met missense_variant 0.19 pretomanid
delamanid
clofazimine
fbiC 1304893 p.Gly655Ser missense_variant 0.22 pretomanid
delamanid
clofazimine
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.99 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1471862 n.17T>G non_coding_transcript_exon_variant 0.98 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1471984 n.139T>A non_coding_transcript_exon_variant 0.14 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472023 n.178G>T non_coding_transcript_exon_variant 0.14 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472034 n.189T>C non_coding_transcript_exon_variant 0.14 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472042 n.197T>C non_coding_transcript_exon_variant 0.15 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrs 1472061 n.216A>T non_coding_transcript_exon_variant 0.14 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin
amikacin Uncertain significance
rrl 1474632 n.975G>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1474717 n.1060A>C non_coding_transcript_exon_variant 0.13 capreomycin
linezolid
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474950 n.1293G>A non_coding_transcript_exon_variant 0.18 capreomycin
linezolid
rrl 1474956 n.1299C>T non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474960 n.1303C>A non_coding_transcript_exon_variant 0.19 capreomycin
linezolid
rrl 1474961 n.1307_1308delTG non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474965 n.1308G>C non_coding_transcript_exon_variant 0.2 capreomycin
linezolid
rrl 1474999 n.1342C>G non_coding_transcript_exon_variant 0.24 capreomycin
linezolid
rrl 1475006 n.1349A>G non_coding_transcript_exon_variant 0.23 capreomycin
linezolid
rrl 1475031 n.1374G>A non_coding_transcript_exon_variant 0.21 capreomycin
linezolid
rrl 1475061 n.1404C>T non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid
rrl 1475213 n.1556C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid
rrl 1475315 n.1658A>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid
rrl 1475429 n.1772G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475460 n.1803A>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475483 n.1826C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475629 n.1972G>A non_coding_transcript_exon_variant 0.15 capreomycin
linezolid
rrl 1475659 n.2002G>A non_coding_transcript_exon_variant 0.18 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475763 n.2106C>A non_coding_transcript_exon_variant 0.14 capreomycin
linezolid
rrl 1476529 n.2872A>G non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid
inhA 1674006 c.-196T>C upstream_gene_variant 0.14 isoniazid
ethionamide
inhA 1674036 c.-166G>A upstream_gene_variant 0.14 isoniazid
ethionamide
inhA 1674037 c.-165C>A upstream_gene_variant 0.14 isoniazid
ethionamide
inhA 1674045 c.-157G>C upstream_gene_variant 0.14 isoniazid
ethionamide
inhA 1674049 c.-153C>G upstream_gene_variant 0.14 isoniazid
ethionamide
inhA 1674054 c.-148T>C upstream_gene_variant 0.14 isoniazid
ethionamide
inhA 1674060 c.-142A>C upstream_gene_variant 0.14 isoniazid
ethionamide
inhA 1674069 c.-133G>C upstream_gene_variant 0.13 isoniazid
ethionamide
inhA 1674070 c.-132G>A upstream_gene_variant 0.13 isoniazid
ethionamide
inhA 1674079 c.-123C>G upstream_gene_variant 0.14 isoniazid
ethionamide
inhA 1674471 c.270G>T synonymous_variant 0.16 isoniazid
ethionamide
inhA 1674486 c.285T>C synonymous_variant 0.18 isoniazid
ethionamide
inhA 1674489 c.288G>C synonymous_variant 0.18 isoniazid
ethionamide
inhA 1674542 p.Ala114Glu missense_variant 0.17 isoniazid
ethionamide
inhA 1674546 c.345T>C synonymous_variant 0.16 isoniazid
ethionamide
inhA 1674549 c.348G>C synonymous_variant 0.15 isoniazid
ethionamide
inhA 1674579 c.378G>C synonymous_variant 0.18 isoniazid
ethionamide
inhA 1674585 c.384T>C synonymous_variant 0.21 isoniazid
ethionamide
rpsA 1833613 c.72C>A synonymous_variant 0.15 pyrazinamide
rpsA 1833634 c.93G>A synonymous_variant 0.16 pyrazinamide
rpsA 1833646 c.105T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
rpsA 1833667 c.126C>G synonymous_variant 0.17 pyrazinamide
rpsA 1833724 c.183C>G synonymous_variant 0.16 pyrazinamide
rpsA 1833727 c.186G>C synonymous_variant 0.15 pyrazinamide
rpsA 1833739 c.198C>A synonymous_variant 0.18 pyrazinamide
rpsA 1833742 c.201A>G synonymous_variant 0.17 pyrazinamide
rpsA 1833745 c.204G>C synonymous_variant 0.18 pyrazinamide
rpsA 1833790 c.249T>C synonymous_variant 0.19 pyrazinamide
rpsA 1833793 c.252C>T synonymous_variant 0.18 pyrazinamide
rpsA 1833811 c.270G>T synonymous_variant 0.19 pyrazinamide
rpsA 1833841 c.300C>G synonymous_variant 0.2 pyrazinamide
rpsA 1833847 c.306C>G synonymous_variant 0.19 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.19 pyrazinamide
rpsA 1833862 c.321G>C synonymous_variant 0.16 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.15 pyrazinamide
rpsA 1833953 c.412C>T synonymous_variant 0.14 pyrazinamide
rpsA 1834555 c.1014T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834609 c.1068T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834639 c.1098T>C synonymous_variant 0.15 pyrazinamide
tsnR 1853361 c.-245T>C upstream_gene_variant 0.14 linezolid
tsnR 1853974 c.369C>T synonymous_variant 1.0 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 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
ndh 2102240 p.Arg268His missense_variant 0.99 isoniazid Not assoc w R - Interim
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.99 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.99 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 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
Rv1979c 2223553 c.-389C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
folC 2747468 p.Asp44Gly missense_variant 0.98 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
lpqB 3625258 c.-348G>C upstream_gene_variant 0.23 rifampicin
bedaquiline
mtrB 3625267 c.1347T>C synonymous_variant 0.22 rifampicin Not assoc w R - Interim
bedaquiline
mtrB 3626467 c.147G>A synonymous_variant 1.0 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
rpoA 3878052 c.456C>T synonymous_variant 0.14 rifampicin
rpoA 3878055 c.453A>G synonymous_variant 0.14 rifampicin
rpoA 3878118 c.390T>C synonymous_variant 0.15 rifampicin
rpoA 3878130 c.378C>G synonymous_variant 0.15 rifampicin
rpoA 3878163 c.345C>T synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878175 c.333G>C synonymous_variant 0.14 rifampicin
rpoA 3878187 c.321C>G synonymous_variant 0.16 rifampicin
rpoA 3878193 c.315T>C synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878199 c.309T>C synonymous_variant 0.15 rifampicin
rpoA 3878202 c.306G>C synonymous_variant 0.15 rifampicin
rpoA 3878217 c.291A>G synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoA 3878235 c.273G>A synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878244 c.264G>A synonymous_variant 0.16 rifampicin
rpoA 3878247 c.261G>C synonymous_variant 0.16 rifampicin
rpoA 3878256 c.252G>C synonymous_variant 0.16 rifampicin
rpoA 3878264 p.Ser82Gly missense_variant 0.15 rifampicin
rpoA 3878265 c.243G>A synonymous_variant 0.16 rifampicin
rpoA 3878271 c.237T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878276 c.232C>T synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878283 p.Glu75Asp missense_variant 0.18 rifampicin Uncertain significance
rpoA 3878292 c.216T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878304 c.204G>C synonymous_variant 0.17 rifampicin
rpoA 3878322 c.186A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878331 c.177A>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878337 c.171T>C synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoA 3878358 c.150C>G synonymous_variant 0.2 rifampicin
rpoA 3878364 c.144A>T synonymous_variant 0.19 rifampicin
rpoA 3878381 c.127C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoA 3878397 c.111G>A synonymous_variant 0.16 rifampicin
rpoA 3878415 c.93C>T synonymous_variant 0.17 rifampicin
rpoA 3878424 c.84G>C synonymous_variant 0.15 rifampicin
rpoA 3878442 c.66G>C synonymous_variant 0.13 rifampicin
rpoA 3879022 c.-515G>C upstream_gene_variant 0.14 rifampicin
rpoA 3879040 c.-533G>T upstream_gene_variant 0.16 rifampicin
rpoA 3879061 c.-554C>T upstream_gene_variant 0.16 rifampicin
rpoA 3879079 c.-572A>G upstream_gene_variant 0.14 rifampicin
clpC1 4038347 c.2358G>C synonymous_variant 0.14 pyrazinamide
clpC1 4038353 c.2352G>A synonymous_variant 0.14 pyrazinamide
clpC1 4038356 c.2349T>C synonymous_variant 0.15 pyrazinamide
clpC1 4038359 c.2346A>G synonymous_variant 0.14 pyrazinamide
clpC1 4038368 c.2337T>C synonymous_variant 0.17 pyrazinamide
clpC1 4038374 c.2331C>T synonymous_variant 0.18 pyrazinamide
clpC1 4038388 c.2317T>C synonymous_variant 0.19 pyrazinamide
clpC1 4038392 c.2313C>T synonymous_variant 0.19 pyrazinamide
clpC1 4038395 c.2310C>G synonymous_variant 0.19 pyrazinamide
clpC1 4038398 c.2307G>T synonymous_variant 0.17 pyrazinamide
clpC1 4038403 c.2302T>C synonymous_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4038410 c.2295C>T synonymous_variant 0.17 pyrazinamide
clpC1 4038419 c.2286T>C synonymous_variant 0.2 pyrazinamide
clpC1 4038433 c.2272C>T synonymous_variant 0.19 pyrazinamide
clpC1 4038436 p.Ala757Ser missense_variant 0.2 pyrazinamide
clpC1 4038444 p.Ala754Lys missense_variant 0.16 pyrazinamide
clpC1 4038446 c.2259T>C synonymous_variant 0.16 pyrazinamide
clpC1 4038456 p.Val750Glu missense_variant 0.16 pyrazinamide
clpC1 4038530 p.Glu725Asp missense_variant 0.17 pyrazinamide
clpC1 4038536 c.2169C>T synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
clpC1 4039601 c.1104G>A synonymous_variant 0.17 pyrazinamide
clpC1 4039610 c.1095G>C synonymous_variant 0.15 pyrazinamide
clpC1 4039991 c.714G>T synonymous_variant 0.14 pyrazinamide
clpC1 4040018 c.687G>C synonymous_variant 0.16 pyrazinamide
clpC1 4040033 c.672G>C synonymous_variant 0.15 pyrazinamide
clpC1 4040042 c.663C>A synonymous_variant 0.15 pyrazinamide
clpC1 4040057 c.648C>T synonymous_variant 0.15 pyrazinamide
clpC1 4040063 c.642G>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.96 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
panD 4044174 c.108C>G synonymous_variant 0.14 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 1.0 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 4240657 c.795G>T synonymous_variant 0.14 ethambutol
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4240678 c.816T>G synonymous_variant 0.14 ethambutol
embC 4240685 p.Thr275Ala missense_variant 0.14 ethambutol
embC 4240698 p.Ala279Gly missense_variant 0.14 ethambutol
embC 4240723 c.861C>G synonymous_variant 0.16 ethambutol
embC 4241042 p.Asn394Asp missense_variant 0.91 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4248098 p.Ile529Phe missense_variant 0.16 ethambutol
embB 4248119 p.Ser536Ala missense_variant 0.17 ethambutol
embB 4248122 p.Leu537Val missense_variant 0.16 ethambutol
embB 4248133 c.1620C>G synonymous_variant 0.17 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 0.18 ethambutol Not assoc w R - Interim
embB 4248172 c.1659G>C synonymous_variant 0.17 ethambutol
embB 4248205 c.1692C>A synonymous_variant 0.17 ethambutol
embB 4248206 p.Ser565Gly missense_variant 0.16 ethambutol Uncertain significance
embB 4248217 c.1704C>T synonymous_variant 0.17 ethambutol
embB 4248220 c.1707A>G synonymous_variant 0.17 ethambutol Not assoc w R - Interim
embB 4248241 c.1728C>T synonymous_variant 0.17 ethambutol
embB 4248252 p.Gly580Ala missense_variant 0.15 ethambutol
aftB 4267960 p.Val293Met missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.99 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 1.0 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
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 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407799 p.Val135Ala missense_variant 1.0 streptomycin
gid 4407848 p.Ala119Thr missense_variant 1.0 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.99 streptomycin Not assoc w R