TB-Profiler result

Run: ERR4813206
Summary

Run ID: ERR4813206

Sample name:

Date: 20-10-2023 05:08:59

Number of reads: 3225912

Percentage reads mapped: 99.59

Strain: lineage4.1.1

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.Val170Phe (1.00), rpoB p.Gln429Pro (0.99)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Thr142Ala (1.00)
Streptomycin R gid c.102delG (1.00)
Fluoroquinolones R gyrA p.Asp94Asn (1.00)
Moxifloxacin R gyrA p.Asp94Asn (1.00)
Ofloxacin R gyrA p.Asp94Asn (1.00)
Levofloxacin R gyrA p.Asp94Asn (1.00)
Ciprofloxacin R gyrA p.Asp94Asn (1.00)
Aminoglycosides
Amikacin
Capreomycin R tlyA c.430dupA (0.98), tlyA c.430dupA (0.98)
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 760314 p.Val170Phe missense_variant 1.0 rifampicin
rpoB 761092 p.Gln429Pro missense_variant 0.99 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
tlyA 1918368 c.430dupA frameshift_variant 0.98 capreomycin, capreomycin
pncA 2288818 p.Thr142Ala missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4408100 c.102delG 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
gyrB 6052 p.Ile271Met missense_variant 1.0
gyrB 7221 p.Ser661Thr missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 761268 p.Ile488Leu missense_variant 0.99
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416699 p.Leu217Val missense_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
inhA 1673865 c.-337C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G 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
embC 4242803 p.Val981Leu missense_variant 0.98
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0