TB-Profiler result

Run: SRR17657932
Summary

Run ID: SRR17657932

Sample name:

Date: 01-02-2024 22:22:23

Number of reads: 9918016

Percentage reads mapped: 99.67

Strain: lineage4

Drug-resistance: HR-TB

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R ahpC c.-52C>T (1.00)
Ethambutol R embB p.Gly406Asp (1.00), embB p.Asp1024Asn (1.00)
Pyrazinamide R pncA p.Thr76Pro (1.00)
Streptomycin R gid p.Glu173* (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA p.Cys131* (1.00)
Clofazimine
Para-aminosalicylic_acid R folC p.Ile43Thr (1.00)
Delamanid
Bedaquiline
Linezolid
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family Main Spoligotype RDs Frequency
lineage4 Euro-American LAM;T;S;X;H None 1.0
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
pncA 2289016 p.Thr76Pro missense_variant 1.0 pyrazinamide
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
folC 2747471 p.Ile43Thr missense_variant 1.0 para-aminosalicylic_acid
embB 4247730 p.Gly406Asp missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
ethA 4327081 p.Cys131* stop_gained 1.0 ethionamide
gid 4407686 p.Glu173* stop_gained 1.0 streptomycin
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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8147 p.Asn282Lys missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304501 p.Ala524Gly missense_variant 1.0
fbiC 1305357 c.2427C>G synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154277 p.Asp612Gly missense_variant 1.0
katG 2155141 p.Thr324Leu missense_variant 1.0
PPE35 2168742 p.Gly624Asp missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290088 c.-847G>A upstream_gene_variant 1.0
Rv2752c 3065482 p.Cys237Tyr missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612113 c.1003dupG frameshift_variant 1.0
rpoA 3878609 c.-102T>A upstream_gene_variant 0.14
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4246401 p.Val1057Met missense_variant 1.0
embB 4247675 p.Ala388Thr missense_variant 1.0
ethA 4327376 p.Ala33Gly missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0