TB-Profiler result

Run: ERR2516541
Summary

Run ID: ERR2516541

Sample name:

Date: 19-10-2023 23:46:17

Number of reads: 2562385

Percentage reads mapped: 99.78

Strain: lineage4

Drug-resistance: 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.Leu430Arg (1.00), rpoB p.Asp435Tyr (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gly406Ser (1.00)
Pyrazinamide R pncA c.380_388delAGGTCGATG (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Asn (1.00)
Moxifloxacin R gyrA p.Asp94Asn (1.00)
Ofloxacin R gyrA p.Asp94Asn (1.00)
Levofloxacin R gyrA p.Asp94Asn (1.00)
Ciprofloxacin R gyrA p.Asp94Asn (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
Ethionamide R ethA c.341dupA (1.00), ethA c.341dupA (1.00)
Clofazimine R mmpR5 c.198dupG (1.00)
Para-aminosalicylic_acid
Delamanid
Bedaquiline R mmpR5 c.198dupG (1.00)
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 7581 p.Asp94Asn missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761095 p.Leu430Arg missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
mmpR5 779181 c.198dupG frameshift_variant 1.0 clofazimine, bedaquiline
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288853 c.380_388delAGGTCGATG disruptive_inframe_deletion 1.0 pyrazinamide
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4327132 c.341dupA 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
mshA 575837 c.490C>T synonymous_variant 1.0
rpoB 761889 p.Val695Leu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777875 c.605delG frameshift_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rplC 801009 c.201A>G synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
ndh 2101831 c.1212G>A synonymous_variant 1.0
katG 2156173 c.-62C>A upstream_gene_variant 1.0
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ahpC 2726141 c.-52C>A upstream_gene_variant 1.0
Rv2752c 3065517 c.675C>T synonymous_variant 1.0
thyA 3074495 c.-24C>T upstream_gene_variant 1.0
Rv3083 3449351 c.849dupG frameshift_variant 1.0
fprA 3474299 p.Asp98Gly missense_variant 1.0
Rv3236c 3612219 p.Val300Ile missense_variant 1.0
rpoA 3878635 c.-128C>T upstream_gene_variant 0.31
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4328317 c.-844C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407631 p.Cys191Phe missense_variant 1.0
gid 4407967 p.Leu79Trp missense_variant 1.0