TB-Profiler result

Run: ERR2516492

Summary

Run ID: ERR2516492

Sample name:

Date: 19-10-2023 23:47:44

Number of reads: 2978656

Percentage reads mapped: 99.72

Strain: lineage4.3.3

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.Ser450Gln (1.00)
Isoniazid R inhA p.Ser94Ala (1.00), ahpC c.-52C>T (1.00)
Ethambutol R embB p.Gly406Ser (1.00)
Pyrazinamide R pncA p.Gly97Ser (1.00)
Streptomycin
Fluoroquinolones R gyrB p.Ser447Phe (1.00)
Moxifloxacin R gyrB p.Ser447Phe (1.00)
Ofloxacin R gyrB p.Ser447Phe (1.00)
Levofloxacin R gyrB p.Ser447Phe (1.00)
Ciprofloxacin R gyrB p.Ser447Phe (1.00)
Aminoglycosides R rrs n.1401A>G (0.82)
Amikacin R rrs n.1401A>G (0.82), eis c.-14C>T (0.16)
Capreomycin R rrs n.1401A>G (0.82)
Kanamycin R rrs n.1401A>G (0.82), eis c.-14C>T (0.16)
Cycloserine
Ethionamide R inhA p.Ser94Ala (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 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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
gyrB 6579 p.Ser447Phe missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761154 p.Ser450Gln missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.82 kanamycin, capreomycin, aminoglycosides, amikacin
inhA 1674481 p.Ser94Ala missense_variant 1.0 isoniazid, ethionamide
pncA 2288953 p.Gly97Ser missense_variant 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.16 kanamycin, amikacin
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4247729 p.Gly406Ser 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576128 c.781C>T synonymous_variant 1.0
rpoC 764363 p.Gly332Ser missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 1.0
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
rpsA 1833585 p.Asp15Ala missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154727 p.Ile462Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyX 3067680 p.Cys89Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3612626 p.Ala164Val missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248161 c.1648C>T synonymous_variant 1.0
ethA 4326713 p.Gln254Pro missense_variant 1.0
whiB6 4338596 c.-76_-75delAGinsC upstream_gene_variant 1.0
gid 4407956 p.Arg83Gly missense_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0