TB-Profiler result

Run: ERR4828844
Summary

Run ID: ERR4828844

Sample name:

Date: 20-10-2023 15:24:12

Number of reads: 2473559

Percentage reads mapped: 99.66

Strain: lineage4

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.Ser450Trp (1.00)
Isoniazid R katG c.371dupG (0.58), ahpC c.-54C>T (1.00)
Ethambutol R embB p.Met306Leu (1.00)
Pyrazinamide R pncA p.Thr168Asn (1.00)
Streptomycin R gid c.115delC (1.00)
Fluoroquinolones R gyrA p.Ala90Val (1.00), gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Ala90Val (1.00), gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Ala90Val (1.00), gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Ala90Val (1.00), gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Ala90Val (1.00), gyrA p.Asp94Gly (1.00)
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
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 1.0 rifampicin
katG 2155740 c.371dupG frameshift_variant 0.58 isoniazid
pncA 2288739 p.Thr168Asn missense_variant 1.0 pyrazinamide
ahpC 2726139 c.-54C>T upstream_gene_variant 1.0 isoniazid
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol
gid 4408087 c.115delC frameshift_variant 1.0 streptomycin
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 9171 p.Val624Leu missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777050 c.1431G>C synonymous_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 2154915 c.1197A>G synonymous_variant 1.0
PPE35 2169383 c.1230C>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.98
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4245572 c.-942C>T upstream_gene_variant 1.0
ubiA 4269296 p.Met180Val missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408358 c.-156C>G upstream_gene_variant 1.0