TB-Profiler result

Run: ERR234631
Summary

Run ID: ERR234631

Sample name:

Date: 19-10-2023 18:01:08

Number of reads: 3459176

Percentage reads mapped: 99.56

Strain: lineage4.1.2.1

Drug-resistance: MDR-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.Ser428Arg (0.93), rpoB p.His445Tyr (0.90)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Asp354Ala (0.97)
Pyrazinamide
Streptomycin R rpsL p.Lys88Arg (0.97)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.754_755dupGC (0.86), ethA c.754_755dupGC (0.86)
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 0.96
lineage4.1.2 Euro-American T;H None 0.95
lineage4.1.2.1 Euro-American (Haarlem) T1;H1 RD182 0.95
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
rpoB 761090 p.Ser428Arg missense_variant 0.93 rifampicin
rpoB 761139 p.His445Tyr missense_variant 0.9 rifampicin
rpsL 781822 p.Lys88Arg missense_variant 0.97 streptomycin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
embB 4247574 p.Asp354Ala missense_variant 0.97 ethambutol
ethA 4326718 c.754_755dupGC frameshift_variant 0.86 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 5085 c.-155C>T upstream_gene_variant 0.16
gyrB 5743 c.504G>T synonymous_variant 0.92
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 0.94
mshA 575679 p.Asn111Ser missense_variant 0.99
rpoB 760115 c.309C>T synonymous_variant 0.93
rpoC 765150 p.Gly594Glu missense_variant 0.97
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
rpsA 1833603 p.Asp21Gly missense_variant 0.92
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 0.95
eis 2714277 c.1056T>C synonymous_variant 0.99
folC 2747195 p.Asp135Ala missense_variant 0.95
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 0.95
whiB6 4338595 c.-75delG upstream_gene_variant 1.0