TB-Profiler result

Run: ERR4812973
Summary

Run ID: ERR4812973

Sample name:

Date: 20-10-2023 05:04:24

Number of reads: 4285773

Percentage reads mapped: 99.65

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.His445Asn (0.27), rpoB p.Ser450Leu (0.70)
Isoniazid R fabG1 c.-15C>T (0.80), inhA p.Ile21Thr (0.79), katG p.Ser315Thr (0.30)
Ethambutol R embB p.Met306Ile (0.31), embB p.Gly406Asp (0.82)
Pyrazinamide R pncA p.Gly132Ser (0.15), pncA p.His51Arg (0.80)
Streptomycin
Fluoroquinolones R gyrA p.Ala90Val (0.27)
Moxifloxacin R gyrA p.Ala90Val (0.27)
Ofloxacin R gyrA p.Ala90Val (0.27)
Levofloxacin R gyrA p.Ala90Val (0.27)
Ciprofloxacin R gyrA p.Ala90Val (0.27)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.80), inhA p.Ile21Thr (0.79)
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
lineage4.3 Euro-American (LAM) mainly-LAM None 1.0
lineage4.3.3 Euro-American (LAM) LAM;T RD115 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 0.27 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asn missense_variant 0.27 rifampicin
rpoB 761155 p.Ser450Leu missense_variant 0.7 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.8 isoniazid, ethionamide
inhA 1674263 p.Ile21Thr missense_variant 0.79 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.3 isoniazid
pncA 2288848 p.Gly132Ser missense_variant 0.15 pyrazinamide
pncA 2289090 p.His51Arg missense_variant 0.8 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.31 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.82 ethambutol
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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G 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
rpsA 1834683 p.Ala381Val missense_variant 0.81
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918100 p.Val54Gly missense_variant 0.72
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288819 p.Gln141His missense_variant 0.17
kasA 2518919 p.Gly269Ser missense_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
embC 4242182 p.Ala774Ser missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407768 p.Leu145Phe missense_variant 0.75
gid 4407973 p.Val77Gly missense_variant 0.25
gid 4408156 p.Leu16Arg missense_variant 1.0