TB-Profiler result

Run: ERR10610170

Summary

Run ID: ERR10610170

Sample name:

Date: 22-05-2023 22:15:38

Number of reads: 129073

Percentage reads mapped: 98.41

Strain: lineage4.3.2.1

Drug-resistance: HR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.09
lineage4.3.2 Euro-American (LAM) LAM3 None 0.09
lineage4.3.2.1 Euro-American (LAM) LAM3 RD761 0.06
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
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 5662 c.423C>T synonymous_variant 0.67
gyrB 6423 p.Trp395* stop_gained 0.67
gyrA 7222 c.-80C>T upstream_gene_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
mmpL5 776780 p.Leu567Phe missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsA 1833545 p.Pro2Thr missense_variant 0.29
rpsA 1833726 p.Val62Ala missense_variant 0.22
katG 2154988 p.Pro375Arg missense_variant 1.0
katG 2155551 c.561G>T synonymous_variant 0.29
katG 2156558 c.-447G>T upstream_gene_variant 0.67
pepQ 2860552 c.-134C>T upstream_gene_variant 0.25
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3087048 p.Pro77Ala missense_variant 0.33
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840625 p.Leu266Ile missense_variant 0.67
alr 3840690 p.Pro244His missense_variant 1.0
ddn 3987084 p.Gly81Cys missense_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 1.0
clpC1 4040229 p.Gly159Val missense_variant 0.4
embA 4243822 p.Thr197Met missense_variant 0.67
embB 4245605 c.-909G>T upstream_gene_variant 1.0
whiB6 4338384 c.138C>T synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0