TB-Profiler result

Run: ERR1971860
Summary

Run ID: ERR1971860

Sample name:

Date: 2025-05-06T19:09:19.128272

Number of reads: 3152236

Percentage reads mapped: 99.45

Median coverage: 179.0

Strain: lineage7

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage7 Lineage 7 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
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 8876 c.1575C>T synonymous_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
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
Rv0010c 13445 c.114G>A synonymous_variant 1.0 isoniazid Not assoc w R - Interim
Rv0010c 13563 c.-5A>G upstream_gene_variant 1.0 isoniazid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
Rv0565c 656656 p.Ala272Val missense_variant 1.0 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 1.0 ethionamide Uncertain significance
mmaA3 737363 p.Glu263* stop_gained 1.0 isoniazid Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764013 p.Glu215Ala missense_variant 1.0 rifampicin Uncertain significance
rpoC 766955 p.Glu1196Lys missense_variant 1.0 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
mmpL5 776202 p.Gly760Ala missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781488 c.-72G>A upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 800307 c.-502_-501insCGCGACAAGGC upstream_gene_variant 1.0 linezolid Uncertain significance
Rv1129c 1253515 c.1020C>T synonymous_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1253707 c.828A>C synonymous_variant 1.0 isoniazid Not assoc w R - Interim
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Not assoc w R - Interim
Rv1129c 1254136 p.Glu133Asp missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
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
fbiC 1305129 c.2199C>T synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
sigE 1364575 p.Arg55Cys missense_variant 1.0 pyrazinamide Uncertain significance
embR 1416977 p.His124Arg missense_variant 1.0 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 1.0 ethambutol Uncertain significance
embR 1417838 c.-491C>A upstream_gene_variant 0.99 ethambutol Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1474959 n.1303_1304insAC non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
rpsA 1834916 p.Thr459Pro missense_variant 1.0 pyrazinamide 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
tlyA 1918281 c.342A>C synonymous_variant 1.0 capreomycin Uncertain significance
bacA 2062922 p.Ile603Val missense_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Not assoc w R
ndh 2102218 c.825C>T synonymous_variant 0.99 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
ndh 2103185 c.-143A>G upstream_gene_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
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 2169232 p.Thr461Ala missense_variant 1.0 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
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid Uncertain significance
Rv2681 2996887 p.Gly50Glu missense_variant 0.99 capreomycin Uncertain significance
Rv2681 2998027 p.Ala430Val missense_variant 1.0 capreomycin Uncertain significance
Rv2752c 3065880 c.312C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
isoniazid Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
Rv3083 3448540 p.Gly13Ser missense_variant 1.0 ethionamide Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3627386 c.-774delC upstream_gene_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
rpoA 3878040 c.468T>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3878138 p.His124Tyr missense_variant 1.0 rifampicin Uncertain significance
glpK 4138377 p.Val460Ala missense_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
embC 4240153 c.291G>A synonymous_variant 1.0 ethambutol Not assoc w R - Interim
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Not assoc w R
embB 4248073 c.1560C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
aftB 4267649 c.1188T>C synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.99 ethambutol Not assoc w R
ethA 4328371 c.-898C>T upstream_gene_variant 1.0 ethionamide Uncertain significance
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