TB-Profiler result

Run: SRR6824486

Summary

Run ID: SRR6824486

Sample name:

Date: 20-10-2023 19:48:27

Number of reads: 11003648

Percentage reads mapped: 98.81

Strain: lineage4.5

Drug-resistance: MDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Val170Phe (1.00)
Isoniazid R fabG1 c.-17G>T (0.99), katG p.Thr380Ile (1.00), ahpC c.-54C>T (0.99)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Gln122* (1.00)
Streptomycin R rpsL p.Lys43Arg (0.99)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-17G>T (0.99)
Clofazimine
Para-aminosalicylic_acid
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
lineage4.5 Euro-American H;T RD122 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
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
fabG1 1673423 c.-17G>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2154973 p.Thr380Ile missense_variant 1.0 isoniazid
pncA 2288878 p.Gln122* stop_gained 1.0 pyrazinamide
ahpC 2726139 c.-54C>T upstream_gene_variant 0.99 isoniazid
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576056 p.Val237Arg missense_variant 0.98
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoC 764817 p.Val483Gly missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777353 c.1128G>A synonymous_variant 0.99
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2290077 c.-836G>T upstream_gene_variant 1.0
ald 3087860 c.1041A>G synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3841364 c.57C>T synonymous_variant 0.99
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0