TB-Profiler result

Run: ERR1034611
Summary

Run ID: ERR1034611

Sample name:

Date: 20-10-2023 22:03:14

Number of reads: 25602700

Percentage reads mapped: 99.66

Strain: lineage4.8

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.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (0.96), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (1.00), embB p.Gly406Asp (0.95)
Pyrazinamide R pncA p.Gly97Ser (0.96)
Streptomycin R rpsL p.Lys43Arg (0.96)
Fluoroquinolones R gyrB p.Ser447Phe (0.97)
Moxifloxacin R gyrB p.Ser447Phe (0.97)
Ofloxacin R gyrB p.Ser447Phe (0.97)
Levofloxacin R gyrB p.Ser447Phe (0.97)
Ciprofloxacin R gyrB p.Ser447Phe (0.97)
Aminoglycosides R rrs n.1401A>G (0.97)
Amikacin R rrs n.1401A>G (0.97)
Capreomycin R rrs n.1401A>G (0.97)
Kanamycin R rrs n.1401A>G (0.97)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.96), ethA c.299delT (0.94), ethA c.299delT (0.94)
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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.96
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
gyrB 6579 p.Ser447Phe missense_variant 0.97 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.96 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.97 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.96 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288953 p.Gly97Ser missense_variant 0.96 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.95 ethambutol
ethA 4327174 c.299delT frameshift_variant 0.94 ethionamide, 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
rpoC 764616 p.Asn416Ser missense_variant 0.96
rpoC 765331 c.1962C>T synonymous_variant 0.96
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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.95
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.95
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3087759 c.942delC frameshift_variant 0.87
ald 3087805 p.Trp329* stop_gained 0.11
Rv3083 3448497 c.-7T>A upstream_gene_variant 0.24
Rv3083 3448500 c.-4A>G upstream_gene_variant 0.19
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.96