TB-Profiler result

Run: SRR29274261
Summary

Run ID: SRR29274261

Sample name:

Date: 2025-02-11T18:42:45.927291

Number of reads: 2126601

Percentage reads mapped: 99.67

Median coverage: 68.0

Strain: lineage4.2.1;lineage4.8

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.2 Euro-American None 0.13
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.89
lineage4.2.1 Euro-American (TUR) None 0.12
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.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Ser297Ala Uncertain significance Mutation from literature
p.Gly406Asp Assoc w R
pyrazinamide pncA p.His137Pro Assoc w R - Interim
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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 1.0 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.24 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.13 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288832 p.His137Pro missense_variant 0.86 pyrazinamide Assoc w R - Interim
embB 4247402 p.Ser297Ala missense_variant 0.12 ethambutol Uncertain significance Mutation from literature
embB 4247730 p.Gly406Asp missense_variant 0.91 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 0.23 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491247 c.465C>T synonymous_variant 0.2 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
rpoC 764817 p.Val483Gly missense_variant 0.12 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val 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
rplC 800204 c.-605T>C upstream_gene_variant 0.11 linezolid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin 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
ddn 3987221 p.Leu126Phe missense_variant 0.88 pretomanid
delamanid
embC 4242493 c.2631G>C synonymous_variant 0.93 ethambutol Not assoc w R - Interim
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326632 p.His281Pro missense_variant 0.14 ethionamide Uncertain significance
ethA 4328214 c.-741C>T upstream_gene_variant 0.93 ethionamide
whiB6 4338424 p.Val33Asp missense_variant 0.76 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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 0.13 kanamycin
capreomycin
amikacin
whiB6 4338863 c.-342C>G upstream_gene_variant 0.91 kanamycin
capreomycin
amikacin
gid 4408099 p.Leu35Gln missense_variant 0.93 streptomycin Uncertain significance