TB-Profiler result

Run: SRR671868
Summary

Run ID: SRR671868

Sample name:

Date: 20-10-2023 21:50:54

Number of reads: 6116898

Percentage reads mapped: 99.45

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.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol
Pyrazinamide R pncA p.Pro62Leu (0.35)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
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 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
pncA 2289057 p.Pro62Leu missense_variant 0.35 pyrazinamide
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
ccsA 620029 c.139C>T synonymous_variant 1.0
ccsA 620566 p.Asp226Asn missense_variant 1.0
rpoB 759648 c.-159_-158insT upstream_gene_variant 1.0
rpoC 764931 p.Ala521Val missense_variant 0.11
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777254 c.1227G>A synonymous_variant 1.0
mmpL5 777640 c.832_840dupGCCATCTTC conservative_inframe_insertion 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 800678 c.-131C>T upstream_gene_variant 1.0
fbiC 1304387 p.Arg486His missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170371 p.Thr81Asn missense_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 0.99
Rv1979c 2221768 p.His466Arg missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288857 p.Asp129Asn missense_variant 0.12
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
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
embA 4243225 c.-8C>T upstream_gene_variant 1.0
embA 4243830 p.Gly200Ser missense_variant 1.0
embB 4247573 p.Asp354Asn missense_variant 1.0
embB 4248548 p.Ala679Thr missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0