TB-Profiler result

Run: SRR25827330

Summary

Run ID: SRR25827330

Sample name:

Date: 2024-03-26T22:14:02.200575

Number of reads: 2382639

Percentage reads mapped: 49.85

Median coverage: 71.0

Strain: 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 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 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.Ser450Leu Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Gly406Asp Assoc w R
pyrazinamide
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
embB 4247730 p.Gly406Asp missense_variant 1.0 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
Rv0565c 656265 c.1204_1205delAC frameshift_variant 1.0 ethionamide Uncertain significance
nusG 734658 c.405A>G synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 766691 p.Gly1108Ser missense_variant 0.81 rifampicin Uncertain significance
rpoC 766945 c.3576A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 766972 c.3603G>C synonymous_variant 0.2 rifampicin
rpoC 766975 c.3606C>T synonymous_variant 0.2 rifampicin Not assoc w R - Interim
rpoC 766996 c.3627C>T synonymous_variant 0.21 rifampicin Not assoc w R - Interim
rpoC 767002 c.3633G>C synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.22 rifampicin
rpoC 767059 c.3690T>G synonymous_variant 0.28 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.27 rifampicin
rpoC 767098 c.3729T>C synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767119 c.3750A>G synonymous_variant 0.13 rifampicin Not assoc w R - Interim
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
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0 capreomycin Not assoc w R
linezolid Not assoc w R
rpsA 1834303 c.762T>G synonymous_variant 0.12 pyrazinamide
rpsA 1834306 c.765T>C synonymous_variant 0.14 pyrazinamide
rpsA 1834336 c.795C>G synonymous_variant 0.2 pyrazinamide
rpsA 1834339 c.798C>T synonymous_variant 0.2 pyrazinamide
rpsA 1834348 c.807T>C synonymous_variant 0.21 pyrazinamide Not assoc w R - Interim
rpsA 1834366 c.825A>G synonymous_variant 0.23 pyrazinamide Not assoc w R - Interim
rpsA 1834369 c.828C>G synonymous_variant 0.23 pyrazinamide
rpsA 1834375 c.834G>A synonymous_variant 0.23 pyrazinamide
rpsA 1834396 c.855G>C synonymous_variant 0.2 pyrazinamide
rpsA 1834411 c.870T>C synonymous_variant 0.15 pyrazinamide
rpsA 1834417 c.876G>C synonymous_variant 0.14 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168149 p.Pro822Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
ahpC 2726510 p.Leu106Phe missense_variant 1.0 isoniazid Uncertain significance
Rv2680 2995848 c.-257G>A upstream_gene_variant 1.0 capreomycin
Rv3236c 3613636 c.-520A>G upstream_gene_variant 1.0 pyrazinamide Not assoc w R
clpC1 4039729 p.Asp326Asn missense_variant 1.0 pyrazinamide Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ethA 4326977 p.His166Pro missense_variant 0.79 ethionamide Uncertain significance
ethA 4327386 p.Lys30Glu missense_variant 0.25 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