TB-Profiler result

Run: ERR2516534
Summary

Run ID: ERR2516534

Sample name:

Date: 19-10-2023 23:44:45

Number of reads: 4659167

Percentage reads mapped: 99.73

Strain: lineage4

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.Asp435Val (1.00)
Isoniazid R katG p.Ser315Asn (1.00)
Ethambutol R embB p.Gly406Asp (0.99)
Pyrazinamide R pncA c.-11A>G (1.00)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.37)
Moxifloxacin R gyrA p.Ala90Val (0.37)
Ofloxacin R gyrA p.Ala90Val (0.37)
Levofloxacin R gyrA p.Ala90Val (0.37)
Ciprofloxacin R gyrA p.Ala90Val (0.37)
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 ethA p.Tyr408* (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
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 0.37 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Asn missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247730 p.Gly406Asp missense_variant 0.99 ethambutol
ethA 4326250 p.Tyr408* stop_gained 1.0 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 761889 p.Val695Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 0.99
rplC 801009 c.201A>G synonymous_variant 1.0
fbiC 1305486 c.2556C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065517 c.675C>T synonymous_variant 1.0
Rv3083 3448439 c.-64delA upstream_gene_variant 1.0
Rv3083 3448757 p.Ile85Thr missense_variant 1.0
fprA 3474299 p.Asp98Gly missense_variant 1.0
rpoA 3878635 c.-128C>T upstream_gene_variant 0.26
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245025 p.His598Arg missense_variant 1.0
ubiA 4269317 p.Ser173Ala missense_variant 1.0
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0