TB-Profiler result

Run: ERR4799961

Summary

Run ID: ERR4799961

Sample name:

Date: 20-10-2023 04:02:54

Number of reads: 2615731

Percentage reads mapped: 99.66

Strain: lineage4.8

Drug-resistance: 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 (0.95)
Ethambutol R embB p.Met306Leu (1.00)
Pyrazinamide R pncA p.Ile133Thr (0.99)
Streptomycin R rrs n.514A>C (1.00)
Fluoroquinolones R gyrA p.Asp94Gly (0.94)
Moxifloxacin R gyrA p.Asp94Gly (0.94)
Ofloxacin R gyrA p.Asp94Gly (0.94)
Levofloxacin R gyrA p.Asp94Gly (0.94)
Ciprofloxacin R gyrA p.Asp94Gly (0.94)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.99)
Clofazimine
Para-aminosalicylic_acid R folC p.Ile43Thr (0.98)
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.10)
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 0.97
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 7582 p.Asp94Gly missense_variant 0.94 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rplC 801268 p.Cys154Arg missense_variant 0.1 linezolid
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.95 isoniazid
pncA 2288844 p.Ile133Thr missense_variant 0.99 pyrazinamide
folC 2747471 p.Ile43Thr missense_variant 0.98 para-aminosalicylic_acid
embB 4247429 p.Met306Leu missense_variant 1.0 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
rpoC 766466 p.Glu1033Lys missense_variant 0.99
rpoC 766867 c.3498C>T synonymous_variant 0.98
mmpL5 775639 p.Ile948Val missense_variant 0.99
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 0.97
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 0.96
embC 4240061 p.Phe67Val missense_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407670 p.Met178Arg missense_variant 0.97
ald 3086364 c.-455_*2032del transcript_ablation 0.97
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.97