TB-Profiler result

Run: SRR5710013
Summary

Run ID: SRR5710013

Sample name:

Date: 20-10-2023 16:46:45

Number of reads: 3217261

Percentage reads mapped: 99.59

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 (1.00)
Ethambutol R embB p.Met306Ile (0.34), embB p.Gln497Arg (0.78)
Pyrazinamide R pncA c.390_391dupGG (0.22), pncA c.390_391dupGG (0.22), pncA c.166_167dupGA (0.25), pncA p.Leu4Ser (0.17)
Streptomycin R gid p.Glu173* (1.00)
Fluoroquinolones R gyrA p.Asp94Ala (0.99)
Moxifloxacin R gyrA p.Asp94Ala (0.99)
Ofloxacin R gyrA p.Asp94Ala (0.99)
Levofloxacin R gyrA p.Asp94Ala (0.99)
Ciprofloxacin R gyrA p.Asp94Ala (0.99)
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 1.0
lineage4.4.2 Euro-American T1;T2 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 7582 p.Asp94Ala missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288850 c.390_391dupGG frameshift_variant 0.22 pyrazinamide, pyrazinamide
pncA 2289074 c.166_167dupGA frameshift_variant 0.25 pyrazinamide
pncA 2289231 p.Leu4Ser missense_variant 0.17 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.34 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.78 ethambutol
gid 4407686 p.Glu173* stop_gained 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 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
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 1.0
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 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407789 c.414G>A synonymous_variant 1.0