TB-Profiler result

Run: SRR28498467
Summary

Run ID: SRR28498467

Sample name:

Date: 2024-05-22T09:09:15.696307

Number of reads: 2937897

Percentage reads mapped: 99.43

Median coverage: 92.0

Strain: lineage4.1.2.1;lineage4.2.1

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 0.41
lineage4.1.2 Euro-American None 0.37
lineage4.2 Euro-American None 0.59
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.37
lineage4 Euro-American None 1.0
lineage4.2.1 Euro-American (TUR) None 0.6
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
pyrazinamide
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
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 0.64 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.52 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.57 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 0.61 isoniazid Assoc w R High-level resistance
eis 2715344 c.-12C>T upstream_gene_variant 0.6 kanamycin Assoc w R
embB 4247402 p.Ser297Ala missense_variant 0.57 ethambutol 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
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 491247 c.465C>T synonymous_variant 0.63 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
fgd1 491591 p.Lys270Met missense_variant 0.34 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.48 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 619969 p.Val27Ile missense_variant 0.55 capreomycin Not assoc w R - Interim
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.39 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.42 rifampicin Not assoc w R
rpoC 764817 p.Val483Gly missense_variant 0.59 rifampicin Uncertain significance
rpoC 765150 p.Gly594Glu missense_variant 0.47 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 781276 c.-284A>C upstream_gene_variant 0.45 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800204 c.-605T>C upstream_gene_variant 0.64 linezolid
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 2063685 c.1044G>A synonymous_variant 0.54 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063911 p.Ile273Thr missense_variant 0.67 streptomycin Uncertain significance
kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
PPE35 2169879 p.Phe245Cys missense_variant 0.52 pyrazinamide Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289070 p.Phe58Val missense_variant 0.6 pyrazinamide Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.38 isoniazid
Rv2680 2996136 p.Ser11Asn missense_variant 0.19 capreomycin
ald 3086742 c.-78A>C upstream_gene_variant 0.52 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
lpqB 3623222 c.1689A>G synonymous_variant 0.5 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4039606 p.Glu367Gln missense_variant 0.37 pyrazinamide Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.43 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 0.53 ethambutol Not assoc w R
embA 4243813 p.Arg194Gln missense_variant 0.4 ethambutol Uncertain significance
embB 4249594 c.3081G>A synonymous_variant 0.57 ethambutol Not assoc w R - Interim
ubiA 4269721 p.Ala38Val missense_variant 0.61 ethambutol Uncertain significance
ethA 4326632 p.His281Pro missense_variant 0.6 ethionamide Uncertain significance
ethA 4328376 c.-903G>C upstream_gene_variant 0.63 ethionamide
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 4408103 p.Gly34Arg missense_variant 0.4 streptomycin Uncertain significance