TB-Profiler result

Run: ERR4810977
Summary

Run ID: ERR4810977

Sample name:

Date: 20-10-2023 00:13:34

Number of reads: 8869631

Percentage reads mapped: 99.46

Strain: lineage4.5

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.Phe424Val (1.00), rpoB p.Leu430Pro (1.00)
Isoniazid
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Thr168Asn (0.22), pncA p.Thr135Pro (0.37), pncA p.Pro62Leu (0.13), pncA p.Tyr34* (0.18)
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
lineage4.5 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
gyrA 7570 p.Ala90Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761076 p.Phe424Val missense_variant 1.0 rifampicin
rpoB 761095 p.Leu430Pro missense_variant 1.0 rifampicin
pncA 2288739 p.Thr168Asn missense_variant 0.22 pyrazinamide
pncA 2288839 p.Thr135Pro missense_variant 0.37 pyrazinamide
pncA 2289057 p.Pro62Leu missense_variant 0.13 pyrazinamide
pncA 2289140 p.Tyr34* stop_gained 0.18 pyrazinamide
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
gyrB 5524 c.285C>G synonymous_variant 1.0
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
rpoC 765653 p.Arg762Cys missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779296 p.Gly103Ser missense_variant 1.0
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
katG 2155418 p.Pro232Ala missense_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289039 c.191_202delATTCCTCGTCGT disruptive_inframe_deletion 0.13
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 4245131 c.1899G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0