TB-Profiler result

Run: ERR4829238
Summary

Run ID: ERR4829238

Sample name:

Date: 2025-09-15T14:54:23.669479

Number of reads: 2328261

Percentage reads mapped: 30.9

Median coverage: 46.0

Strain: lineage3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 100.0
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
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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9596 c.2295G>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9777 p.Asn826Asp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13277 c.282T>C synonymous_variant 1.0 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657267 c.204G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
nusG 734354 p.Pro34Leu missense_variant 1.0 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 1.0 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoB 762636 p.Lys944Glu missense_variant 1.0 rifampicin Not assoc w R
rpoB 762872 p.Met1022Ile missense_variant 0.3 rifampicin Uncertain significance
rpoB 762878 p.Ile1024Met missense_variant 0.34 rifampicin Uncertain significance
rpoB 762879 p.Met1025Leu missense_variant 0.39 rifampicin Uncertain significance
rpoC 762896 c.-474G>C upstream_gene_variant 0.44 rifampicin Uncertain significance
rpoB 762917 c.3111C>G synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 762923 c.3117C>G synonymous_variant 0.46 rifampicin Not assoc w R - Interim
rpoB 762925 p.Thr1040Ile missense_variant 0.44 rifampicin Uncertain significance
rpoB 762929 c.3123G>C synonymous_variant 0.44 rifampicin Not assoc w R - Interim
rpoB 762939 p.Met1045Leu missense_variant 0.38 rifampicin Uncertain significance
rpoB 762942 p.Ile1046Val missense_variant 0.34 rifampicin Uncertain significance
rpoC 762956 c.-414G>C upstream_gene_variant 0.29 rifampicin Uncertain significance
rpoC 762965 c.-405T>C upstream_gene_variant 0.27 rifampicin Uncertain significance
rpoC 762980 c.-390T>C upstream_gene_variant 0.28 rifampicin Uncertain significance
rpoC 762989 c.-381G>C upstream_gene_variant 0.29 rifampicin Uncertain significance
rpoB 762995 c.3189G>T synonymous_variant 0.27 rifampicin Not assoc w R - Interim
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764181 p.Asp271Gly missense_variant 1.0 rifampicin Not assoc w R
rpoC 764611 c.1242G>C synonymous_variant 0.32 rifampicin Uncertain significance
rpoC 764632 c.1263T>C synonymous_variant 0.32 rifampicin Not assoc w R - Interim
rpoC 764650 c.1281G>C synonymous_variant 0.27 rifampicin Uncertain significance
rpoC 764665 c.1296C>T synonymous_variant 0.19 rifampicin Uncertain significance
rpoC 764668 c.1299C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 764671 c.1302G>C synonymous_variant 0.2 rifampicin Uncertain significance
rpoC 764672 p.Gln435Glu missense_variant 0.19 rifampicin Uncertain significance
rpoC 764677 c.1308C>G synonymous_variant 0.18 rifampicin Not assoc w R - Interim
rpoC 764695 c.1326T>C synonymous_variant 0.2 rifampicin Uncertain significance
rpoC 764701 c.1332C>G synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoC 764705 p.Leu446Lys missense_variant 0.15 rifampicin Uncertain significance
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
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 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472172 n.327T>C non_coding_transcript_exon_variant 0.6 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472214 n.369C>G non_coding_transcript_exon_variant 0.74 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472235 n.390G>C non_coding_transcript_exon_variant 0.71 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472240 n.395G>C non_coding_transcript_exon_variant 0.69 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472242 n.397C>T non_coding_transcript_exon_variant 0.69 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472251 n.406G>A non_coding_transcript_exon_variant 0.68 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472253 n.408G>T non_coding_transcript_exon_variant 0.69 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472259 n.414C>A non_coding_transcript_exon_variant 0.68 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472266 n.421C>A non_coding_transcript_exon_variant 0.67 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472277 n.432C>G non_coding_transcript_exon_variant 0.38 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472713 n.868T>C non_coding_transcript_exon_variant 0.17 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472715 n.870C>T non_coding_transcript_exon_variant 0.17 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472716 n.871C>T non_coding_transcript_exon_variant 0.17 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472734 n.889C>T non_coding_transcript_exon_variant 0.33 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472741 n.896G>A non_coding_transcript_exon_variant 0.31 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472742 n.897C>T non_coding_transcript_exon_variant 0.38 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472781 n.936C>T non_coding_transcript_exon_variant 0.37 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472793 n.948A>T non_coding_transcript_exon_variant 0.24 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472803 n.958T>A non_coding_transcript_exon_variant 0.24 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472812 n.967A>C non_coding_transcript_exon_variant 0.2 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473051 n.1206T>C non_coding_transcript_exon_variant 0.12 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473053 n.1208T>G non_coding_transcript_exon_variant 0.12 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473062 n.1217T>A non_coding_transcript_exon_variant 0.14 amikacin Not assoc w R
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1473719 n.62G>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473721 n.64G>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473731 n.74T>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473736 n.79C>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473745 n.89delT non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473748 n.91A>G non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473750 n.93C>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473756 n.99G>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473758 n.101G>T non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473764 n.107G>A non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1473765 n.108A>G non_coding_transcript_exon_variant 0.25 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475129 n.1472G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476336 n.2679C>G non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>G non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.24 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>A non_coding_transcript_exon_variant 0.19 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476567 n.2910C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476569 n.2912G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476573 n.2916A>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
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
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2170769 c.-157C>T upstream_gene_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289047 c.195C>T synonymous_variant 1.0 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 1.0 pyrazinamide Uncertain significance
eis 2714784 c.549C>T synonymous_variant 1.0 amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
eis 2714915 c.418C>T synonymous_variant 1.0 amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
eis 2715432 c.-100C>T upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726105 c.-88G>A upstream_gene_variant 1.0 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 1.0 amikacin Not assoc w R
ethambutol Not assoc w R
kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
rpoA 3877752 c.756C>T synonymous_variant 1.0 rifampicin Not assoc w R - Interim
clpC1 4040033 c.672G>C synonymous_variant 0.12 pyrazinamide Uncertain significance
clpC1 4040045 c.660C>G synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4040048 c.657C>T synonymous_variant 0.15 pyrazinamide Not assoc w R - Interim
clpC1 4040069 c.636G>C synonymous_variant 0.16 pyrazinamide Uncertain significance
clpC1 4040072 c.633C>T synonymous_variant 0.15 pyrazinamide Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 1.0 pyrazinamide Uncertain significance
glpK 4138622 c.1134C>T synonymous_variant 1.0 ethambutol Not assoc w R
isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
streptomycin Not assoc w R - Interim
embC 4242075 p.Arg738Gln missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R