TB-Profiler result

Run: ERR11488597
Summary

Run ID: ERR11488597

Sample name:

Date: 10-01-2024 18:45:03

Number of reads: 13801835

Percentage reads mapped: 99.52

Strain: lineage4.1.1.3

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 (1.00), katG p.Ser315Thr (0.99)
Ethambutol R embA c.-16C>G (1.00), embB p.Met306Ile (1.00)
Pyrazinamide R pncA p.Arg154Gly (1.00)
Streptomycin R rrs n.878G>A (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.25), gyrA p.Asp94Asn (0.67)
Moxifloxacin R gyrA p.Ala90Val (0.25), gyrA p.Asp94Asn (0.67)
Ofloxacin R gyrA p.Ala90Val (0.25), gyrA p.Asp94Asn (0.67)
Levofloxacin R gyrA p.Ala90Val (0.25), gyrA p.Asp94Asn (0.67)
Ciprofloxacin R gyrA p.Ala90Val (0.25), gyrA p.Asp94Asn (0.67)
Aminoglycosides
Amikacin
Capreomycin R tlyA c.16dupC (0.21), tlyA c.391dupC (0.44), tlyA c.391dupC (0.44), tlyA c.397dupC (0.18), tlyA c.397dupC (0.18)
Kanamycin R eis c.-37G>T (1.00)
Cycloserine R ald c.464delG (1.00)
Ethionamide R fabG1 c.-15C>T (1.00), ethA c.1192_1194dupGTG (0.98), ethA c.869dupA (1.00), ethA c.869dupA (1.00)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 1.0
lineage4.1.1.3 Euro-American (X-type) X1;X3 RD193 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 0.25 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7581 p.Asp94Asn missense_variant 0.67 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1472723 n.878G>A non_coding_transcript_exon_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
tlyA 1917952 c.16dupC frameshift_variant 0.21 capreomycin
tlyA 1918328 c.391dupC frameshift_variant 0.44 capreomycin, capreomycin
tlyA 1918335 c.397dupC frameshift_variant 0.18 capreomycin, capreomycin
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2288782 p.Arg154Gly missense_variant 1.0 pyrazinamide
eis 2715369 c.-37G>T upstream_gene_variant 1.0 kanamycin
ald 3087278 c.464delG frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247431 p.Met306Ile missense_variant 1.0 ethambutol
ethA 4326279 c.1192_1194dupGTG conservative_inframe_insertion 0.98 ethionamide
ethA 4326604 c.869dupA frameshift_variant 1.0 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoB 762285 p.Arg827Cys missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rpsL 781435 c.-125G>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
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407798 c.405G>T synonymous_variant 1.0