TB-Profiler result

Run: ERR4799628
Summary

Run ID: ERR4799628

Sample name:

Date: 20-10-2023 03:54:26

Number of reads: 2986031

Percentage reads mapped: 99.66

Strain: lineage4.3.4.1

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.Ser450Leu (1.00)
Isoniazid R fabG1 c.-8T>C (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.His137Pro (0.98)
Streptomycin R rpsL p.Lys88Met (0.99)
Fluoroquinolones R gyrA p.Ala90Val (0.95)
Moxifloxacin R gyrA p.Ala90Val (0.95)
Ofloxacin R gyrA p.Ala90Val (0.95)
Levofloxacin R gyrA p.Ala90Val (0.95)
Ciprofloxacin R gyrA p.Ala90Val (0.95)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-8T>C (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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.4 Euro-American (LAM) LAM RD174 0.98
lineage4.3.4.1 Euro-American (LAM) LAM1;LAM2 RD174 0.98
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 0.95 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781822 p.Lys88Met missense_variant 0.99 streptomycin
fabG1 1673432 c.-8T>C upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288832 p.His137Pro missense_variant 0.98 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761277 p.Ile491Val missense_variant 1.0
rpoC 762506 c.-864C>T upstream_gene_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.98
mmpL5 775639 p.Ile948Val 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
ndh 2103205 c.-163G>A upstream_gene_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726323 p.Pro44Arg missense_variant 0.95
thyA 3073868 p.Thr202Ala missense_variant 0.97
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612009 p.Ala370Thr missense_variant 1.0
fbiA 3640661 p.Gln40Arg missense_variant 0.98
clpC1 4038287 c.2418C>T synonymous_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407966 p.Leu79Phe missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0