TB-Profiler result

Run: ERR4811368

Summary

Run ID: ERR4811368

Sample name:

Date: 20-10-2023 00:46:01

Number of reads: 8052604

Percentage reads mapped: 99.3

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.Ser450Leu (0.96)
Isoniazid R katG p.Ser315Thr (0.98)
Ethambutol R embB p.Met306Ile (0.96)
Pyrazinamide R pncA p.Ser104Gly (0.98)
Streptomycin R rpsL p.Lys88Arg (0.98)
Fluoroquinolones R gyrB p.Ala504Thr (0.94), gyrA p.Asp94Gly (0.97)
Moxifloxacin R gyrB p.Ala504Thr (0.94), gyrA p.Asp94Gly (0.97)
Ofloxacin R gyrB p.Ala504Thr (0.94), gyrA p.Asp94Gly (0.97)
Levofloxacin R gyrB p.Ala504Thr (0.94), gyrA p.Asp94Gly (0.97)
Ciprofloxacin R gyrB p.Ala504Thr (0.94), gyrA p.Asp94Gly (0.97)
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
gyrB 6749 p.Ala504Thr missense_variant 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 0.96 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.98 streptomycin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2288932 p.Ser104Gly missense_variant 0.98 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.96 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 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 490718 c.-65G>T upstream_gene_variant 0.97
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoB 762549 p.Gly915Ser missense_variant 0.96
rpoC 765638 p.Glu757Lys missense_variant 0.97
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
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2222879 p.Val96Ile missense_variant 0.99
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
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
whiB6 4338473 c.49A>C synonymous_variant 0.98
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338705 c.-184A>G upstream_gene_variant 0.98