TB-Profiler result

Run: ERR2510419

Summary

Run ID: ERR2510419

Sample name:

Date: 20-10-2023 07:06:13

Number of reads: 1249898

Percentage reads mapped: 99.51

Strain: lineage4.2.2.2

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.Thr427Ile (1.00), rpoB p.Asp435Tyr (1.00), rpoB p.Asn437Tyr (0.56)
Isoniazid R fabG1 c.-15C>T (0.42), fabG1 c.-8T>C (0.53), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Asp328Tyr (1.00), embB p.Tyr334His (0.18)
Pyrazinamide R pncA c.61dupG (0.53), pncA c.50dupG (0.46), pncA c.50dupG (0.46)
Streptomycin R gid c.115delC (1.00)
Fluoroquinolones R gyrA p.Ala90Val (1.00)
Moxifloxacin R gyrA p.Ala90Val (1.00)
Ofloxacin R gyrA p.Ala90Val (1.00)
Levofloxacin R gyrA p.Ala90Val (1.00)
Ciprofloxacin R gyrA p.Ala90Val (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.42), fabG1 c.-8T>C (0.53)
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.99
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR 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
rpoB 761086 p.Thr427Ile missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
rpoB 761115 p.Asn437Tyr missense_variant 0.56 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.42 isoniazid, ethionamide
fabG1 1673432 c.-8T>C upstream_gene_variant 0.53 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289180 c.61dupG frameshift_variant 0.53 pyrazinamide
pncA 2289191 c.50dupG frameshift_variant 0.46 pyrazinamide, pyrazinamide
embB 4247495 p.Asp328Tyr missense_variant 1.0 ethambutol
embB 4247513 p.Tyr334His missense_variant 0.18 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 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 1.0
rpoB 761489 c.1683G>A 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
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2103027 c.15delA frameshift_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 1.0
ald 3086788 c.-32T>C 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
ethA 4326419 p.Ala352Glu missense_variant 0.42
whiB6 4338595 c.-75delG upstream_gene_variant 1.0