TB-Profiler result

Run: ERR4799106
Summary

Run ID: ERR4799106

Sample name:

Date: 20-10-2023 03:36:01

Number of reads: 2890944

Percentage reads mapped: 99.5

Strain: lineage4.2.2.2

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 (0.14)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA c.29dupA (0.98)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Gly (0.99)
Moxifloxacin R gyrA p.Asp94Gly (0.99)
Ofloxacin R gyrA p.Asp94Gly (0.99)
Levofloxacin R gyrA p.Asp94Gly (0.99)
Ciprofloxacin R gyrA p.Asp94Gly (0.99)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.14), ethA c.125_128delGCGG (0.97), ethA c.125_128delGCGG (0.97)
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
lineage4.2 Euro-American H;T;LAM None 0.98
lineage4.2.2 Euro-American (Ural) T;LAM7-TUR None 0.86
lineage4.2.2.2 Euro-American (Ural) T;LAM7-TUR None 0.98
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 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.14 isoniazid, ethionamide
pncA 2289212 c.29dupA frameshift_variant 0.98 pyrazinamide
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
ethA 4327345 c.125_128delGCGG frameshift_variant 0.97 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
gyrB 5784 p.Thr182Ile missense_variant 0.98
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 8688 p.Ala463Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576077 c.730C>T synonymous_variant 0.97
rpoB 761489 c.1683G>A synonymous_variant 1.0
rpoC 766466 p.Glu1033Lys missense_variant 0.18
rpoC 766825 p.Lys1152Asn missense_variant 0.2
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776402 c.2079C>G synonymous_variant 0.97
mmpR5 779149 p.Glu54Lys missense_variant 0.98
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
katG 2154952 p.Asp387Gly missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3066280 c.-89C>T upstream_gene_variant 1.0
ald 3086742 c.-78A>C upstream_gene_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
alr 3840952 p.Lys157Glu missense_variant 0.95
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407956 p.Arg83Gly missense_variant 0.15