TB-Profiler result

Run: SRR28351442
Summary

Run ID: SRR28351442

Sample name:

Date: 2024-05-22T14:09:31.561990

Number of reads: 774608

Percentage reads mapped: 95.32

Median coverage: 18.0

Strain: lineage3.1

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.96
lineage3.1 East-African-Indian RD750 0.33
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
c.451_453delGTCinsCG Assoc w R High-level resistance
c.346_348delCACinsGG Assoc w R High-level resistance
c.316_318delGCGinsTC Assoc w R High-level resistance
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
katG 2155168 p.Ser315Thr missense_variant 0.78 isoniazid Assoc w R High-level resistance
katG 2155659 c.451_453delGTCinsCG frameshift_variant&missense_variant 0.63 isoniazid Assoc w R High-level resistance
katG 2155764 c.346_348delCACinsGG frameshift_variant&missense_variant 0.86 isoniazid Assoc w R High-level resistance
katG 2155794 c.316_318delGCGinsTC frameshift_variant&missense_variant 0.7 isoniazid Assoc w R High-level resistance
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 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 7607 c.306C>G synonymous_variant 0.55 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7613 c.312G>A synonymous_variant 0.62 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 7622 c.321C>T synonymous_variant 0.65 levofloxacin
moxifloxacin
gyrA 7631 c.330G>C synonymous_variant 0.69 levofloxacin
moxifloxacin
gyrA 7637 c.336C>T synonymous_variant 0.69 levofloxacin
moxifloxacin
gyrA 7652 c.351C>T synonymous_variant 0.71 levofloxacin
moxifloxacin
gyrA 7658 c.357A>G synonymous_variant 0.69 levofloxacin
moxifloxacin
gyrA 7661 c.360C>T synonymous_variant 0.69 levofloxacin
moxifloxacin
gyrA 7664 c.363T>C synonymous_variant 0.69 levofloxacin
moxifloxacin
gyrA 7667 c.366C>T synonymous_variant 0.67 levofloxacin
moxifloxacin
gyrA 7670 c.369A>G synonymous_variant 0.69 levofloxacin
moxifloxacin
gyrA 7673 c.372G>A synonymous_variant 0.69 levofloxacin
moxifloxacin
gyrA 7676 c.375G>C synonymous_variant 0.69 levofloxacin
moxifloxacin
gyrA 7679 c.378G>C synonymous_variant 0.69 levofloxacin
moxifloxacin
gyrA 7683 c.382_384delAGGinsCT frameshift_variant&missense_variant 0.7 levofloxacin
moxifloxacin
gyrA 7694 c.393A>G synonymous_variant 0.67 levofloxacin
moxifloxacin
gyrA 7697 c.396C>G synonymous_variant 0.67 levofloxacin
moxifloxacin
gyrA 7706 c.405C>T synonymous_variant 0.64 levofloxacin
moxifloxacin
gyrA 7709 c.408G>C synonymous_variant 0.67 levofloxacin
moxifloxacin
gyrA 7710 c.409T>C synonymous_variant 0.67 levofloxacin
moxifloxacin
gyrA 7728 c.427_429delAGGinsCC frameshift_variant&missense_variant 0.73 levofloxacin
moxifloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
ccsA 620619 c.729G>C synonymous_variant 0.29 capreomycin
amikacin
kanamycin
ccsA 620625 c.735A>C synonymous_variant 0.33 capreomycin
amikacin
kanamycin
ccsA 620631 c.741T>C synonymous_variant 0.35 capreomycin
amikacin
kanamycin
ccsA 620649 c.759A>G synonymous_variant 0.38 capreomycin
amikacin
kanamycin
ccsA 620652 c.762C>G synonymous_variant 0.38 capreomycin
amikacin
kanamycin
ccsA 620661 c.771C>G synonymous_variant 0.39 capreomycin
amikacin
kanamycin
ccsA 620694 c.804C>G synonymous_variant 0.36 capreomycin
amikacin
kanamycin
ccsA 620698 p.Val270Ile missense_variant 0.36 capreomycin
amikacin
kanamycin
ccsA 620715 c.825C>T synonymous_variant 0.35 capreomycin
amikacin
kanamycin
rpoB 760059 c.253_255delTACinsGA frameshift_variant&missense_variant 0.85 rifampicin
rpoB 760067 c.261G>C synonymous_variant 0.9 rifampicin
rpoB 760070 c.264T>C synonymous_variant 0.91 rifampicin
rpoB 760082 c.276C>T synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoB 760088 c.282C>G synonymous_variant 0.96 rifampicin
rpoB 760091 c.285G>C synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoB 760101 c.295T>C synonymous_variant 0.96 rifampicin Not assoc w R - Interim
rpoB 760104 c.298_300delTCGinsAGC synonymous_variant 0.96 rifampicin
rpoB 760112 c.306T>C synonymous_variant 0.96 rifampicin
rpoB 760118 c.312T>G synonymous_variant 0.98 rifampicin Not assoc w R - Interim
rpoB 760121 c.315T>C synonymous_variant 0.98 rifampicin Not assoc w R - Interim
rpoB 760130 p.Asp108Glu missense_variant 0.98 rifampicin Uncertain significance
rpoB 760136 c.330G>A synonymous_variant 0.99 rifampicin
rpoB 760139 c.333A>T synonymous_variant 0.99 rifampicin
rpoB 760142 c.336C>G synonymous_variant 0.99 rifampicin
rpoB 760178 c.372G>A synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 760181 c.375T>C synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 760184 c.378A>G synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 760196 c.390C>G synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 760235 c.429T>C synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 760244 c.438G>C synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoB 760283 c.477G>C synonymous_variant 0.98 rifampicin Not assoc w R - Interim
rpoB 760298 c.492G>C synonymous_variant 0.98 rifampicin Not assoc w R - Interim
rpoB 760310 c.504G>C synonymous_variant 0.97 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764161 c.792G>C synonymous_variant 0.47 rifampicin
rpoC 764182 p.Asp271Glu missense_variant 0.47 rifampicin Uncertain significance
rpoC 764188 c.819A>G synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 764266 c.897T>C synonymous_variant 0.57 rifampicin
rpoC 764272 c.903G>C synonymous_variant 0.64 rifampicin
rpoC 764278 c.909A>G synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoC 764293 c.924G>C synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoC 764297 p.Met310Leu missense_variant 0.5 rifampicin
rpoC 764380 c.1011G>C synonymous_variant 0.47 rifampicin Not assoc w R - Interim
rpoC 764512 c.1143G>T synonymous_variant 0.42 rifampicin Not assoc w R - Interim
rpoC 764527 c.1158C>T synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 764536 c.1167G>T synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoC 764539 c.1170C>G synonymous_variant 0.57 rifampicin Not assoc w R - Interim
rpoC 764575 c.1206T>G synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoC 764593 c.1224C>T synonymous_variant 0.3 rifampicin
rpoC 764605 c.1236G>C synonymous_variant 0.37 rifampicin Not assoc w R - Interim
rpoC 764611 c.1242G>C synonymous_variant 0.33 rifampicin
rpoC 764611 c.1242G>T synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764623 c.1254C>G synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 764626 c.1257C>T synonymous_variant 0.63 rifampicin Not assoc w R - Interim
rpoC 764632 c.1263T>C synonymous_variant 0.4 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>T synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoC 764701 c.1332C>G synonymous_variant 0.52 rifampicin Not assoc w R - Interim
rpoC 764803 c.1434C>T synonymous_variant 0.53 rifampicin Not assoc w R - Interim
rpoC 764809 c.1440C>T synonymous_variant 0.47 rifampicin Not assoc w R
rpoC 764869 c.1500C>T synonymous_variant 0.5 rifampicin Not assoc w R - Interim
rpoC 764916 p.Leu516Pro missense_variant 0.31 rifampicin Uncertain significance
rpoC 764935 c.1566T>C synonymous_variant 0.35 rifampicin
rpoC 764948 c.1579T>C synonymous_variant 0.39 rifampicin Not assoc w R - Interim
rpoC 765330 p.Ser654Asn missense_variant 0.52 rifampicin Uncertain significance
rpoC 765338 p.Gln657Lys missense_variant 0.81 rifampicin
rpoC 765352 c.1983G>C synonymous_variant 0.84 rifampicin Not assoc w R - Interim
rpoC 765357 p.Met663Thr missense_variant 0.84 rifampicin
rpoC 765361 c.1992C>G synonymous_variant 0.85 rifampicin
rpoC 765383 c.2014_2016delATGinsCC frameshift_variant&missense_variant 0.91 rifampicin
rpoC 765403 c.2034G>C synonymous_variant 0.93 rifampicin
rpoC 765404 p.Leu679Lys missense_variant 0.93 rifampicin
rpoC 765409 c.2040T>C synonymous_variant 0.93 rifampicin
rpoC 765412 c.2043T>C synonymous_variant 0.93 rifampicin
rpoC 765425 p.Lys686Glu missense_variant 0.93 rifampicin
rpoC 765445 c.2076G>C synonymous_variant 0.96 rifampicin Not assoc w R - Interim
rpoC 765452 p.Ala695Arg missense_variant 0.96 rifampicin
rpoC 765466 c.2097C>T synonymous_variant 0.97 rifampicin
rpoC 765478 c.2109T>C synonymous_variant 0.97 rifampicin Not assoc w R - Interim
rpoC 765480 p.Tyr704Phe missense_variant 0.97 rifampicin Uncertain significance
rpoC 765496 c.2127C>G synonymous_variant 0.97 rifampicin
rpoC 765499 c.2130C>G synonymous_variant 0.97 rifampicin Not assoc w R - Interim
rpoC 765529 c.2160C>T synonymous_variant 0.96 rifampicin
rpoC 765533 p.Tyr722His missense_variant 0.96 rifampicin Uncertain significance
rpoC 765547 c.2178C>T synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoC 765548 c.2179_2181delAGCinsTCG synonymous_variant 0.95 rifampicin
rpoC 765553 c.2184C>T synonymous_variant 0.94 rifampicin Not assoc w R - Interim
rpoC 765556 c.2187G>C synonymous_variant 0.95 rifampicin
rpoC 765562 c.2193G>T synonymous_variant 0.95 rifampicin Not assoc w R - Interim
rpoC 765577 c.2208G>T synonymous_variant 0.94 rifampicin
rpoC 765591 p.Arg741Gln missense_variant 0.9 rifampicin
rpoC 765596 p.Lys743Gln missense_variant 0.91 rifampicin
rpoC 765607 c.2238C>G synonymous_variant 0.74 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoC 767104 c.3735C>G synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoC 767105 c.3736_3738delAACinsCG frameshift_variant&missense_variant 0.99 rifampicin
rpoC 767119 c.3750A>G synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoC 767134 c.3765C>T synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoC 767138 c.3769C>T synonymous_variant 0.99 rifampicin Not assoc w R - Interim
rpoC 767158 c.3789T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoC 767162 p.Asn1265Ala missense_variant 0.99 rifampicin
rpoC 767174 p.Asn1269Asp missense_variant 0.98 rifampicin
rpoC 767180 p.Ala1271Gln missense_variant 0.98 rifampicin
rpoC 767191 c.3822C>G synonymous_variant 0.97 rifampicin Not assoc w R - Interim
rpoC 767197 c.3828G>A synonymous_variant 0.97 rifampicin Not assoc w R - Interim
rpoC 767200 c.3831G>A synonymous_variant 0.96 rifampicin
rpoC 767221 c.3852C>G synonymous_variant 0.8 rifampicin Not assoc w R - Interim
rpoC 767230 c.3861G>C synonymous_variant 0.69 rifampicin Not assoc w R - Interim
rpoC 767233 c.3864T>C synonymous_variant 0.62 rifampicin Not assoc w R - Interim
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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
sigE 1364839 c.427T>C synonymous_variant 0.5 pyrazinamide
sigE 1364847 c.435G>C synonymous_variant 0.47 pyrazinamide
sigE 1364865 c.453G>C synonymous_variant 0.3 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472150 n.305T>A non_coding_transcript_exon_variant 0.73 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.67 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rrs 1472973 n.1128A>T non_coding_transcript_exon_variant 0.91 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473084 n.1239T>C non_coding_transcript_exon_variant 0.55 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin
amikacin Uncertain significance
rrs 1473104 n.1259C>T non_coding_transcript_exon_variant 0.8 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473110 n.1265T>G non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473111 n.1266A>G non_coding_transcript_exon_variant 0.79 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473123 n.1278delAinsTC non_coding_transcript_exon_variant 0.8 streptomycin
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrs 1473276 n.1431A>G non_coding_transcript_exon_variant 0.72 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
rrl 1474362 n.705A>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474753 n.1096A>G non_coding_transcript_exon_variant 0.3 capreomycin Uncertain significance
linezolid
rrl 1474760 n.1103A>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474794 n.1137C>T non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474803 n.1146G>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474812 n.1155G>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1474830 n.1173A>G non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475452 n.1795C>A non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476103 n.2446C>G non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid
rrl 1476115 n.2458T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476131 n.2474C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476160 n.2503T>C non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476214 n.2557G>T non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476215 n.2558C>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476224 n.2567A>G non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>A non_coding_transcript_exon_variant 0.32 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476251 n.2594T>G non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid
rrl 1476256 n.2599A>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476281 n.2624T>C non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476299 n.2642C>T non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476540 n.2883C>T non_coding_transcript_exon_variant 0.62 capreomycin Uncertain significance
linezolid
rrl 1476583 n.2926G>A non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid
rrl 1476584 n.2927C>T non_coding_transcript_exon_variant 0.67 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476594 n.2937C>T non_coding_transcript_exon_variant 0.59 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476597 n.2940G>A non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid
rrl 1476603 n.2946G>A non_coding_transcript_exon_variant 0.61 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476628 n.2971T>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476664 n.3007T>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid
rrl 1476665 n.3008T>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid
rrl 1476674 n.3017T>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476679 n.3022T>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid
rrl 1476689 n.3032A>T non_coding_transcript_exon_variant 0.32 capreomycin
linezolid
rrl 1476690 n.3033C>T non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid
rrl 1476695 n.3038T>A non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
fabG1 1673760 p.Lys107Asn missense_variant 0.82 ethionamide
isoniazid
inhA 1673772 c.-430C>A upstream_gene_variant 0.9 ethionamide
isoniazid
inhA 1673778 c.-424C>G upstream_gene_variant 0.92 ethionamide
isoniazid
inhA 1673784 c.-418G>T upstream_gene_variant 0.92 ethionamide
isoniazid
inhA 1673787 c.-415G>C upstream_gene_variant 0.93 ethionamide
isoniazid
inhA 1673799 c.-403T>C upstream_gene_variant 0.93 ethionamide
isoniazid
inhA 1673802 c.-400A>G upstream_gene_variant 0.93 ethionamide
isoniazid
inhA 1673808 c.-394A>C upstream_gene_variant 0.93 ethionamide
isoniazid
fabG1 1673829 p.Asn130Lys missense_variant 0.9 ethionamide
isoniazid
fabG1 1673830 p.Lys131Arg missense_variant 0.9 ethionamide
isoniazid
inhA 1673838 c.-364T>C upstream_gene_variant 0.9 ethionamide
isoniazid
inhA 1673841 c.-361A>G upstream_gene_variant 0.91 ethionamide
isoniazid
fabG1 1673844 p.Met135Ile missense_variant 0.9 ethionamide
isoniazid
inhA 1673847 c.-355A>C upstream_gene_variant 0.9 ethionamide
isoniazid
inhA 1673853 c.-349A>C upstream_gene_variant 0.93 ethionamide
isoniazid
inhA 1673856 c.-346T>C upstream_gene_variant 0.93 ethionamide
isoniazid
inhA 1673859 c.-343G>C upstream_gene_variant 0.93 ethionamide
isoniazid
inhA 1673865 c.-337C>G upstream_gene_variant 0.94 ethionamide
isoniazid
fabG1 1673870 p.Ser144Met missense_variant 0.95 ethionamide
isoniazid
inhA 1673877 c.-325C>G upstream_gene_variant 0.95 ethionamide
isoniazid
fabG1 1673905 p.Ser156Ala missense_variant 0.93 ethionamide
isoniazid
inhA 1673916 c.-286A>C upstream_gene_variant 0.85 ethionamide
isoniazid
fabG1 1673917 p.Val160Leu missense_variant 0.84 ethionamide
isoniazid
inhA 1673922 c.-280T>C upstream_gene_variant 0.84 ethionamide
isoniazid
inhA 1673931 c.-271C>G upstream_gene_variant 0.8 ethionamide
isoniazid
rpsA 1833847 c.306C>G synonymous_variant 0.45 pyrazinamide
rpsA 1833856 c.315A>G synonymous_variant 0.45 pyrazinamide
rpsA 1833859 c.318C>G synonymous_variant 0.35 pyrazinamide
rpsA 1833862 c.321G>T synonymous_variant 0.45 pyrazinamide
rpsA 1833874 c.333T>C synonymous_variant 0.35 pyrazinamide
rpsA 1833886 c.345C>G synonymous_variant 0.33 pyrazinamide
rpsA 1833894 p.Ala118Glu missense_variant 0.39 pyrazinamide
rpsA 1833928 c.387G>C synonymous_variant 0.33 pyrazinamide
rpsA 1833949 c.408T>C synonymous_variant 0.37 pyrazinamide
rpsA 1833970 c.429G>T synonymous_variant 0.36 pyrazinamide
katG 2155668 c.444G>C synonymous_variant 0.65 isoniazid
katG 2155674 c.438G>C synonymous_variant 0.69 isoniazid
katG 2155680 c.432G>A synonymous_variant 0.73 isoniazid
katG 2155691 c.421T>C synonymous_variant 0.76 isoniazid
katG 2155696 p.Ala139Val missense_variant 0.78 isoniazid
katG 2155716 c.396T>G synonymous_variant 0.86 isoniazid
katG 2155722 c.390G>C synonymous_variant 0.83 isoniazid
katG 2155728 c.384G>C synonymous_variant 0.83 isoniazid
katG 2155742 p.Gly124Arg missense_variant 0.86 isoniazid
katG 2155747 p.Ala122Gly missense_variant 0.86 isoniazid
katG 2155749 c.363C>T synonymous_variant 0.86 isoniazid Not assoc w R - Interim
katG 2155752 c.360C>T synonymous_variant 0.89 isoniazid
katG 2155769 p.Ile115Val missense_variant 0.86 isoniazid
katG 2155770 c.342C>G synonymous_variant 0.86 isoniazid
katG 2155782 c.330C>A synonymous_variant 0.86 isoniazid
katG 2155800 c.312G>C synonymous_variant 0.59 isoniazid
katG 2155805 p.Ile103Val missense_variant 0.59 isoniazid Uncertain significance
katG 2155806 c.306T>C synonymous_variant 0.59 isoniazid
katG 2155815 c.297G>C synonymous_variant 0.62 isoniazid
katG 2155824 c.288C>G synonymous_variant 0.42 isoniazid
katG 2155828 p.Tyr95Phe missense_variant 0.39 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.4 pyrazinamide 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
pncA 2289047 c.195C>T synonymous_variant 0.9 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.82 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.87 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
Rv2477c 2783786 p.Arg86His missense_variant 0.7 ethambutol Not assoc w R
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4038551 c.2154C>G synonymous_variant 0.98 pyrazinamide
clpC1 4038563 c.2142C>T synonymous_variant 0.99 pyrazinamide
clpC1 4038584 c.2121G>A synonymous_variant 0.99 pyrazinamide
clpC1 4038587 c.2118C>G synonymous_variant 0.99 pyrazinamide
clpC1 4038596 c.2109A>G synonymous_variant 0.99 pyrazinamide
clpC1 4038602 c.2103G>C synonymous_variant 0.99 pyrazinamide
clpC1 4038623 c.2082A>G synonymous_variant 0.99 pyrazinamide
clpC1 4038640 p.Asp689Asn missense_variant 0.99 pyrazinamide
clpC1 4038647 c.2058T>G synonymous_variant 0.99 pyrazinamide
clpC1 4038658 p.Lys683Gln missense_variant 0.99 pyrazinamide
clpC1 4038660 c.2044_2045delTCinsAG synonymous_variant 0.99 pyrazinamide
clpC1 4038662 c.2043T>C synonymous_variant 0.99 pyrazinamide
clpC1 4038671 c.2034T>G synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
clpC1 4038679 p.Pro676Ala missense_variant 0.99 pyrazinamide
clpC1 4038683 c.2022T>C synonymous_variant 0.99 pyrazinamide Not assoc w R - Interim
clpC1 4038695 c.2010C>G synonymous_variant 0.98 pyrazinamide
clpC1 4038704 c.2001T>C synonymous_variant 0.97 pyrazinamide
clpC1 4038710 c.1995G>C synonymous_variant 0.97 pyrazinamide
clpC1 4038713 c.1992T>C synonymous_variant 0.96 pyrazinamide
clpC1 4038725 c.1980C>G synonymous_variant 0.96 pyrazinamide
clpC1 4038740 c.1965G>C synonymous_variant 0.93 pyrazinamide
clpC1 4039022 c.1683A>G synonymous_variant 0.93 pyrazinamide
clpC1 4039046 c.1659C>T synonymous_variant 0.96 pyrazinamide Not assoc w R - Interim
clpC1 4039064 c.1641C>T synonymous_variant 0.97 pyrazinamide
clpC1 4039067 c.1638G>C synonymous_variant 0.97 pyrazinamide
clpC1 4039079 c.1626C>G synonymous_variant 0.98 pyrazinamide Not assoc w R - Interim
clpC1 4039085 c.1620A>G synonymous_variant 0.97 pyrazinamide
clpC1 4039091 c.1614G>C synonymous_variant 0.97 pyrazinamide
clpC1 4039097 c.1608G>T synonymous_variant 0.97 pyrazinamide
clpC1 4039100 c.1605C>T synonymous_variant 0.97 pyrazinamide Not assoc w R - Interim
clpC1 4039103 c.1602T>C synonymous_variant 0.98 pyrazinamide
clpC1 4039106 c.1599G>C synonymous_variant 0.98 pyrazinamide
clpC1 4039118 c.1587C>A synonymous_variant 0.98 pyrazinamide
clpC1 4039142 c.1563A>G synonymous_variant 0.98 pyrazinamide
clpC1 4039145 c.1560G>C synonymous_variant 0.98 pyrazinamide
clpC1 4039169 c.1536A>G synonymous_variant 0.98 pyrazinamide
clpC1 4039178 c.1527G>C synonymous_variant 0.98 pyrazinamide
clpC1 4039183 c.1522T>C synonymous_variant 0.97 pyrazinamide
clpC1 4039187 c.1518G>T synonymous_variant 0.97 pyrazinamide
clpC1 4039190 c.1515C>G synonymous_variant 0.97 pyrazinamide
clpC1 4039220 c.1485G>C synonymous_variant 0.95 pyrazinamide
clpC1 4039241 c.1464G>C synonymous_variant 0.9 pyrazinamide
clpC1 4039649 c.1056G>C synonymous_variant 0.77 pyrazinamide
clpC1 4039652 c.1053G>C synonymous_variant 0.77 pyrazinamide
clpC1 4039670 c.1035G>C synonymous_variant 0.69 pyrazinamide
clpC1 4039682 c.1023C>G synonymous_variant 0.6 pyrazinamide
clpC1 4039694 c.1011G>C synonymous_variant 0.58 pyrazinamide
clpC1 4039724 c.981A>G synonymous_variant 0.53 pyrazinamide
clpC1 4039733 c.972G>C synonymous_variant 0.56 pyrazinamide
clpC1 4039742 c.963C>T synonymous_variant 0.5 pyrazinamide
clpC1 4039748 c.957G>C synonymous_variant 0.44 pyrazinamide
clpC1 4039751 c.954A>G synonymous_variant 0.41 pyrazinamide
clpC1 4039757 c.948A>G synonymous_variant 0.41 pyrazinamide
clpC1 4039760 c.945T>C synonymous_variant 0.41 pyrazinamide
clpC1 4039769 c.936C>G synonymous_variant 0.66 pyrazinamide
clpC1 4039793 c.912C>G synonymous_variant 0.67 pyrazinamide
clpC1 4039802 c.903G>C synonymous_variant 0.69 pyrazinamide
clpC1 4039817 c.888A>T synonymous_variant 0.72 pyrazinamide
clpC1 4039823 c.882T>C synonymous_variant 0.7 pyrazinamide Not assoc w R - Interim
clpC1 4039829 c.874_876delTTGinsCC frameshift_variant&missense_variant 0.68 pyrazinamide
clpC1 4039832 c.873C>A synonymous_variant 0.68 pyrazinamide
clpC1 4039850 c.855T>C synonymous_variant 0.76 pyrazinamide
clpC1 4039865 c.840T>C synonymous_variant 0.82 pyrazinamide
clpC1 4039883 c.822G>A synonymous_variant 0.61 pyrazinamide
clpC1 4039889 c.816G>C synonymous_variant 0.56 pyrazinamide
clpC1 4039898 c.807C>G synonymous_variant 0.63 pyrazinamide
clpC1 4039904 c.801A>G synonymous_variant 0.74 pyrazinamide
clpC1 4039931 c.774T>C synonymous_variant 0.52 pyrazinamide
clpC1 4039934 c.771G>A synonymous_variant 0.39 pyrazinamide
clpC1 4039937 c.768G>C synonymous_variant 0.33 pyrazinamide
clpC1 4039946 c.759A>T synonymous_variant 0.42 pyrazinamide
clpC1 4039949 c.756G>C synonymous_variant 0.52 pyrazinamide
clpC1 4039952 c.753T>C synonymous_variant 0.52 pyrazinamide
clpC1 4039958 c.747G>C synonymous_variant 0.5 pyrazinamide
clpC1 4040522 c.183T>C synonymous_variant 0.33 pyrazinamide Not assoc w R - Interim
glpK 4138622 c.1134C>T synonymous_variant 0.92 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embB 4247491 c.978G>C synonymous_variant 0.58 ethambutol
embB 4247497 c.984T>C synonymous_variant 0.58 ethambutol
embB 4247511 p.Tyr333Phe missense_variant 0.54 ethambutol
embB 4247527 c.1014G>C synonymous_variant 0.5 ethambutol
embB 4247536 c.1023C>G synonymous_variant 0.5 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
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R