TB-Profiler result

Run: ERR2516579
Summary

Run ID: ERR2516579

Sample name:

Date: 19-10-2023 23:41:40

Number of reads: 3638172

Percentage reads mapped: 99.73

Strain: lineage4.9

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.Asp435Phe (0.98), rpoB p.Ser450Cys (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Gln127Pro (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Trp119* (0.95)
Streptomycin R rrs n.907A>C (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), ethA c.580dupC (0.13), ethA c.580dupC (0.13)
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
lineage4.9 Euro-American (H37Rv-like) T1 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
rpoB 761109 p.Asp435Phe missense_variant 0.98 rifampicin
rpoB 761155 p.Ser450Cys missense_variant 1.0 rifampicin
rrs 1472752 n.907A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
katG 2155732 p.Gln127Pro missense_variant 1.0 isoniazid
pncA 2288886 p.Trp119* stop_gained 0.95 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4326893 c.580dupC frameshift_variant 0.13 ethionamide, ethionamide
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
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
katG 2154377 p.Thr579Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
fprA 3474363 c.357G>A synonymous_variant 1.0
clpC1 4038229 p.Pro826Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407785 p.Ala140Ser missense_variant 1.0