TB-Profiler result

Run: ERR2510595
Summary

Run ID: ERR2510595

Sample name:

Date: 20-10-2023 07:14:27

Number of reads: 3632767

Percentage reads mapped: 99.65

Strain: lineage4.6

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 katG p.Ser315Thr (1.00)
Ethambutol R embA c.-12C>T (1.00)
Pyrazinamide
Streptomycin R rrs n.514A>C (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.32), gyrA p.Asp94Ala (0.19)
Moxifloxacin R gyrA p.Ala90Val (0.32), gyrA p.Asp94Ala (0.19)
Ofloxacin R gyrA p.Ala90Val (0.32), gyrA p.Asp94Ala (0.19)
Levofloxacin R gyrA p.Ala90Val (0.32), gyrA p.Asp94Ala (0.19)
Ciprofloxacin R gyrA p.Ala90Val (0.32), gyrA p.Asp94Ala (0.19)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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
lineage4.6 Euro-American T;LAM None 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 0.32 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 0.19 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472359 n.514A>C non_coding_transcript_exon_variant 1.0 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embA 4243221 c.-12C>T upstream_gene_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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 763644 p.Met92Thr missense_variant 1.0
rpoC 764832 p.Glu488Gly missense_variant 1.0
rpoC 766597 c.3228C>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
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168080 p.Thr845Ala missense_variant 1.0
PPE35 2170198 p.Ala139Thr missense_variant 1.0
PPE35 2170792 c.-180T>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746993 c.606C>T synonymous_variant 1.0
Rv2752c 3064682 c.1509dupG frameshift_variant 0.21
Rv2752c 3065022 c.1169dupC frameshift_variant 0.11
Rv2752c 3065194 c.997dupC frameshift_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3613057 c.60G>T synonymous_variant 0.98
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.404dupT frameshift_variant 1.0