TB-Profiler result

Run: ERR8975760

Summary

Run ID: ERR8975760

Sample name:

Date: 20-10-2023 15:39:56

Number of reads: 5687225

Percentage reads mapped: 99.57

Strain: lineage4.1.2.1

Drug-resistance: Pre-XDR-TB


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.His445Tyr (1.00)
Isoniazid R fabG1 c.-15C>T (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-16C>G (1.00), embB p.Glu405Asp (1.00)
Pyrazinamide R pncA p.His71Tyr (1.00)
Streptomycin R gid p.Ala134Glu (0.99)
Fluoroquinolones R gyrA p.Asp94His (1.00)
Moxifloxacin R gyrA p.Asp94His (1.00)
Ofloxacin R gyrA p.Asp94His (1.00)
Levofloxacin R gyrA p.Asp94His (1.00)
Ciprofloxacin R gyrA p.Asp94His (1.00)
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 R ald c.133delA (1.00)
Ethionamide R fabG1 c.-15C>T (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
lineage4.1.2 Euro-American T;H None 1.0
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 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 7581 p.Asp94His missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr 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 1.0 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289031 p.His71Tyr missense_variant 1.0 pyrazinamide
ald 3086951 c.133delA frameshift_variant 1.0 cycloserine
embA 4243217 c.-16C>G upstream_gene_variant 1.0 ethambutol
embB 4247728 p.Glu405Asp missense_variant 1.0 ethambutol
gid 4407802 p.Ala134Glu missense_variant 0.99 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
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
fgd1 491591 p.Lys270Met missense_variant 1.0
mshA 575679 p.Asn111Ser missense_variant 1.0
rpoB 760115 c.309C>T synonymous_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779127 c.139dupG frameshift_variant 0.88
mmpR5 779430 p.Glu147Asp missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406813 c.528T>C synonymous_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
kasA 2518076 c.-39C>T upstream_gene_variant 1.0
pepQ 2860406 p.Gln5* stop_gained 0.13
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
alr 3840259 p.Tyr388Asp missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4247738 p.Ala409Pro missense_variant 1.0
ethA 4326842 p.Tyr211Ser missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0