TB-Profiler result

Run: ERR1035326
Summary

Run ID: ERR1035326

Sample name:

Date: 20-10-2023 21:40:31

Number of reads: 6221187

Percentage reads mapped: 99.72

Strain: lineage4.7

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.Asp435Phe (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gly406Asp (1.00)
Pyrazinamide R pncA p.Arg148Ser (0.10), pncA c.391dupG (0.86), pncA c.391dupG (0.86)
Streptomycin
Fluoroquinolones R gyrA p.Ala74Ser (1.00), gyrA p.Asp94Ala (0.12)
Moxifloxacin R gyrA p.Ala74Ser (1.00), gyrA p.Asp94Ala (0.12)
Ofloxacin R gyrA p.Ala74Ser (1.00), gyrA p.Asp94Ala (0.12)
Levofloxacin R gyrA p.Ala74Ser (1.00), gyrA p.Asp94Ala (0.12)
Ciprofloxacin R gyrA p.Ala74Ser (1.00), gyrA p.Asp94Ala (0.12)
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
lineage4.7 Euro-American (mainly T) T1;T5 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 7521 p.Ala74Ser missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.12 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761109 p.Asp435Phe missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288800 p.Arg148Ser missense_variant 0.1 pyrazinamide
pncA 2288850 c.391dupG frameshift_variant 0.86 pyrazinamide, pyrazinamide
embB 4247730 p.Gly406Asp 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 6921 p.Val561Ala missense_variant 0.85
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoB 761707 c.1910_1912dupTCG disruptive_inframe_insertion 0.83
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779308 p.Arg107Gly missense_variant 0.93
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrs 1473334 n.1489C>T non_coding_transcript_exon_variant 1.0
rrl 1474294 n.637C>G non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289111 p.Val44Ala missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0