TB-Profiler result

Run: ERR13288870
Summary

Run ID: ERR13288870

Sample name:

Date: 2025-02-11T13:48:25.354275

Number of reads: 4215090

Percentage reads mapped: 99.59

Median coverage: 137.0

Strain: lineage2.2.2;lineage4.1.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.12
lineage4.1 Euro-American None 0.87
lineage4.1.2 Euro-American None 0.86
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.87
lineage2.2.2 East-Asian (Beijing) RD105;RD207 0.1
lineage2.2 East-Asian (Beijing) RD105;RD207 0.12
lineage4 Euro-American None 0.88
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
p.His445Tyr Assoc w R
isoniazid inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
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 embA c.-16C>G Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
p.Glu405Asp Uncertain significance Mutation from literature
pyrazinamide pncA c.517dupG Assoc w R
p.His71Tyr Assoc w R
streptomycin rrs n.514A>C Assoc w R
gid p.Ala134Glu Assoc w R
p.Leu79Ser Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine ald c.133delA Mutation from literature
alr p.Leu113Arg Mutation from literature
ethionamide inhA c.-779G>T Assoc w R - Interim Alias fabG1_c.-17G>T
c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA p.Ala381Pro Uncertain significance Mutation from literature
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 761110 p.Asp435Val missense_variant 0.12 rifampicin Assoc w R
rpoB 761139 p.His445Tyr missense_variant 0.85 rifampicin Assoc w R
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 0.18 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.15 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673423 c.-779G>T upstream_gene_variant 0.16 ethionamide Assoc w R - Interim Alias fabG1_c.-17G>T
isoniazid Assoc w R - Interim Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1673425 c.-777C>T upstream_gene_variant 0.84 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 0.99 isoniazid Assoc w R High-level resistance
pncA 2288724 c.517dupG frameshift_variant 0.12 pyrazinamide Assoc w R
pncA 2289031 p.His71Tyr missense_variant 0.85 pyrazinamide Assoc w R
ald 3086951 c.133delA frameshift_variant 0.89 cycloserine Mutation from literature
alr 3841083 p.Leu113Arg missense_variant 0.14 cycloserine Mutation from literature
embA 4243217 c.-16C>G upstream_gene_variant 0.9 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.16 ethambutol Assoc w R
embB 4247728 p.Glu405Asp missense_variant 0.85 ethambutol Uncertain significance Mutation from literature
ethA 4326333 p.Ala381Pro missense_variant 0.14 ethionamide Uncertain significance Mutation from literature
gid 4407802 p.Ala134Glu missense_variant 0.91 streptomycin Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.18 streptomycin Uncertain significance Mutation from literature
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
dnaA 645 c.645A>C synonymous_variant 0.86 isoniazid 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
fgd1 491591 p.Lys270Met missense_variant 0.86 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.12 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575679 p.Asn111Ser missense_variant 0.86 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.11 ethionamide Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.9 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.91 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.11 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.91 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.14 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406813 c.528T>C synonymous_variant 0.9 streptomycin Not assoc w R - Interim
pyrazinamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
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 0.11 isoniazid 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 2518076 c.-39C>T upstream_gene_variant 0.88 isoniazid
folC 2747370 p.Ser77Ala missense_variant 0.12 para-aminosalicylic_acid
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.23 capreomycin Uncertain significance
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.21 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.25 capreomycin
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.12 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
alr 3840259 p.Tyr388Asp missense_variant 0.88 cycloserine
embC 4239298 c.-565C>T upstream_gene_variant 0.9 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 0.91 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.14 ethambutol Not assoc w R
embB 4247738 p.Ala409Pro missense_variant 0.84 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.1 ethambutol Not assoc w R
ethA 4326842 p.Tyr211Ser missense_variant 0.85 ethionamide 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
whiB6 4338794 c.-273A>G upstream_gene_variant 0.11 kanamycin
capreomycin
amikacin
gid 4407927 p.Glu92Asp missense_variant 0.12 streptomycin Not assoc w R