TB-Profiler result

Run: ERR11082097
Summary

Run ID: ERR11082097

Sample name:

Date: 2024-04-15T06:07:31.293789

Number of reads: 1774917

Percentage reads mapped: 99.56

Median coverage: 50.0

Strain: 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
lineage4.1 Euro-American None 0.16
lineage4.1.2 Euro-American None 0.17
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.23
lineage4 Euro-American 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 rpoB p.Leu430Pro Assoc w R
p.His445Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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.Met306Ile Assoc w R
p.Gly406Asp Assoc w R
pyrazinamide pncA p.Leu4Ser Assoc w R
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA p.Tyr32* Assoc w R
clofazimine
para-aminosalicylic_acid thyX c.-16C>T Mutation from literature
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 761095 p.Leu430Pro missense_variant 0.84 rifampicin Assoc w R
rpoB 761141 p.His445Gln missense_variant 0.88 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
inhA 1673425 c.-777C>T upstream_gene_variant 0.17 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid Assoc w R High-level resistance
pncA 2289231 p.Leu4Ser missense_variant 0.16 pyrazinamide Assoc w R
thyX 3067961 c.-16C>T upstream_gene_variant 0.88 para-aminosalicylic_acid Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.85 ethambutol Assoc w R
embB 4247730 p.Gly406Asp missense_variant 0.16 ethambutol Assoc w R
ethA 4327378 p.Tyr32* stop_gained 0.84 ethionamide 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 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7892 c.591G>A synonymous_variant 0.86 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
ccsA 620619 c.729G>A synonymous_variant 0.88 capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
Rv0565c 657269 p.Ser68Pro missense_variant 0.19 ethionamide Uncertain significance
rpoB 759387 c.-420T>C upstream_gene_variant 0.85 rifampicin
rpoB 760115 c.309C>T synonymous_variant 0.28 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.17 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1258c 1407109 p.Ala78Thr missense_variant 0.94 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
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
bacA 2063464 p.Ser422Thr missense_variant 0.87 streptomycin Uncertain significance
kanamycin
capreomycin
amikacin
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.15 isoniazid
eis 2715338 c.-6G>T upstream_gene_variant 0.21 amikacin Uncertain significance
kanamycin Uncertain significance
ribD 2986827 c.-12G>A upstream_gene_variant 0.19 para-aminosalicylic_acid
thyA 3074365 p.Tyr36Ser missense_variant 0.91 para-aminosalicylic_acid
Rv3236c 3613791 c.-675C>T upstream_gene_variant 0.85 pyrazinamide
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
alr 3841362 p.Thr20Met missense_variant 0.77 cycloserine
rpoA 3878575 c.-68C>T upstream_gene_variant 0.69 rifampicin Not assoc w R
clpC1 4038318 p.Pro796Leu missense_variant 0.89 pyrazinamide Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.13 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 0.21 ethambutol Not assoc w R
ethA 4327310 p.Ser55Cys missense_variant 0.89 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407980 p.Pro75Ser missense_variant 0.62 streptomycin Uncertain significance