TB-Profiler result

Run: ERR2517008

Summary

Run ID: ERR2517008

Sample name:

Date: 19-10-2023 23:20:38

Number of reads: 5479648

Percentage reads mapped: 99.82

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 (0.99), katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gly406Ser (1.00), embB p.Asp1024Asn (1.00)
Pyrazinamide R pncA p.Ala146Val (0.99)
Streptomycin R gid p.Gln125* (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.98)
Moxifloxacin R gyrA p.Ala90Val (0.98)
Ofloxacin R gyrA p.Ala90Val (0.98)
Levofloxacin R gyrA p.Ala90Val (0.98)
Ciprofloxacin R gyrA p.Ala90Val (0.98)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (1.00)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.99)
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 0.99
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 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288805 p.Ala146Val missense_variant 0.99 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 1.0 ethambutol
gid 4407830 p.Gln125* stop_gained 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
rpoC 764817 p.Val483Ala missense_variant 0.99
rpoC 765008 p.Leu547Val missense_variant 0.99
rpoC 766085 p.Pro906Ala missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
atpE 1460992 c.-53A>C upstream_gene_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3087912 c.1097_1104delCCGCCAGC frameshift_variant 0.99
alr 3840764 c.657G>C synonymous_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4327058 p.Gly139Asp missense_variant 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.99