TB-Profiler result

Run: SRR29231413
Summary

Run ID: SRR29231413

Sample name:

Date: 2025-02-11T17:55:52.420420

Number of reads: 1747471

Percentage reads mapped: 99.61

Median coverage: 51.0

Strain: lineage3;lineage4.1.1.1

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 0.23
lineage4.1 Euro-American None 0.78
lineage4.1.1.1 Euro-American (X-type) RD183 0.68
lineage4 Euro-American None 0.78
lineage4.1.1 Euro-American (X-type) None 0.74
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
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 0.36 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
gyrB 7156 c.1917C>T synonymous_variant 0.22 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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
Rv0565c 657081 c.390G>A synonymous_variant 0.29 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.72 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.26 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.29 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.71 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 775676 p.Lys935Asn missense_variant 0.22 bedaquiline
clofazimine Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 0.26 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
rplC 800219 c.-590T>C upstream_gene_variant 0.79 linezolid
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417560 c.-213G>T upstream_gene_variant 0.73 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
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 0.16 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.28 pyrazinamide 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
pncA 2289365 c.-125delC upstream_gene_variant 0.31 pyrazinamide
eis 2714274 c.1059G>A synonymous_variant 0.16 kanamycin
amikacin
ahpC 2726210 c.18T>C synonymous_variant 0.86 isoniazid Not assoc w R - Interim
Rv2477c 2782498 c.1545C>T synonymous_variant 0.29 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2681 2997517 p.Asp260Gly missense_variant 0.79 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626524 c.90A>G synonymous_variant 0.21 rifampicin Not assoc w R - Interim
bedaquiline Not assoc w R - Interim
fbiA 3641447 p.Thr302Met missense_variant 0.73 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
alr 3841292 c.129C>T synonymous_variant 0.8 cycloserine
rpoA 3877553 p.Glu319Lys missense_variant 0.69 rifampicin Not assoc w R
embC 4240897 c.1035C>G synonymous_variant 0.86 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.27 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.69 ethambutol Not assoc w R
embB 4249408 c.2895G>A synonymous_variant 0.66 ethambutol Not assoc w R
aftB 4268493 p.Ala115Val missense_variant 0.77 ethambutol Uncertain significance
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 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.22 streptomycin Not assoc w R