TB-Profiler result

Run: SRR5709866
Summary

Run ID: SRR5709866

Sample name:

Date: 20-10-2023 16:40:20

Number of reads: 5591792

Percentage reads mapped: 99.35

Strain: lineage4.4.2

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.His445Tyr (1.00)
Isoniazid R katG p.Ser315Thr (0.98)
Ethambutol R embB p.Gln497Arg (0.98)
Pyrazinamide R pncA p.Glu181* (0.53)
Streptomycin R gid p.Glu173* (0.99)
Fluoroquinolones R gyrA p.Asp94Ala (0.83), gyrA p.Asp94Gly (0.17)
Moxifloxacin R gyrA p.Asp94Ala (0.83), gyrA p.Asp94Gly (0.17)
Ofloxacin R gyrA p.Asp94Ala (0.83), gyrA p.Asp94Gly (0.17)
Levofloxacin R gyrA p.Asp94Ala (0.83), gyrA p.Asp94Gly (0.17)
Ciprofloxacin R gyrA p.Asp94Ala (0.83), gyrA p.Asp94Gly (0.17)
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
lineage4.4 Euro-American S;T None 0.99
lineage4.4.2 Euro-American T1;T2 None 0.99
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 7582 p.Asp94Ala missense_variant 0.83 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.17 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.98 isoniazid
pncA 2288701 p.Glu181* stop_gained 0.53 pyrazinamide
embB 4248003 p.Gln497Arg missense_variant 0.98 ethambutol
gid 4407686 p.Glu173* stop_gained 0.99 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 9304 p.Gly668Asp missense_variant 1.0
gyrA 9539 c.2238C>T 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
inhA 1673973 c.-229G>C upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289239 c.3G>T start_lost 0.22
Rv2752c 3066099 p.Met31Ile missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
Rv3083 3448348 c.-156G>A upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246508 c.-6G>A upstream_gene_variant 0.98
aftB 4268928 c.-92C>T upstream_gene_variant 0.99
aftB 4269375 c.-539G>A upstream_gene_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407789 c.414G>A synonymous_variant 1.0