TB-Profiler result

Run: ERR3287712
Summary

Run ID: ERR3287712

Sample name:

Date: 20-10-2023 05:49:50

Number of reads: 2974541

Percentage reads mapped: 99.56

Strain: lineage4.1.1

Drug-resistance: Pre-XDR-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.Ile480Val (1.00), rpoB p.Ile491Phe (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Asp354Ala (1.00)
Pyrazinamide R pncA p.His51Tyr (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (1.00)
Moxifloxacin R gyrA p.Ala90Val (1.00)
Ofloxacin R gyrA p.Ala90Val (1.00)
Levofloxacin R gyrA p.Ala90Val (1.00)
Ciprofloxacin R gyrA p.Ala90Val (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761244 p.Ile480Val missense_variant 1.0 rifampicin
rpoB 761277 p.Ile491Phe missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289091 p.His51Tyr missense_variant 1.0 pyrazinamide
embB 4247574 p.Asp354Ala 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
gyrB 6052 p.Ile271Met missense_variant 1.0
gyrB 7221 p.Ser661Thr missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416699 p.Leu217Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074588 c.-117A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4326116 p.Thr453Ile missense_variant 1.0
ethA 4327212 p.Thr88Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408099 p.Leu35Arg missense_variant 1.0