TB-Profiler result

Run: ERR2516598
Summary

Run ID: ERR2516598

Sample name:

Date: 19-10-2023 23:46:25

Number of reads: 5770071

Percentage reads mapped: 99.57

Strain: lineage4.1.1

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.Ser450Leu (1.00)
Isoniazid R ahpC c.-52C>T (1.00)
Ethambutol R embB p.Gln497Arg (1.00)
Pyrazinamide R pncA p.Thr47Ala (0.95)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.98), gyrA p.Asp94Gly (1.00)
Moxifloxacin R gyrA p.Ala90Val (0.98), gyrA p.Asp94Gly (1.00)
Ofloxacin R gyrA p.Ala90Val (0.98), gyrA p.Asp94Gly (1.00)
Levofloxacin R gyrA p.Ala90Val (0.98), gyrA p.Asp94Gly (1.00)
Ciprofloxacin R gyrA p.Ala90Val (0.98), gyrA p.Asp94Gly (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide
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
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 0.98 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
pncA 2289103 p.Thr47Ala missense_variant 0.95 pyrazinamide
ahpC 2726141 c.-52C>T upstream_gene_variant 1.0 isoniazid
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
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 6052 p.Ile271Met missense_variant 1.0
gyrB 7221 p.Ser661Thr missense_variant 1.0
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 765150 p.Gly594Glu missense_variant 1.0
rpoC 766488 p.Pro1040Arg missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416699 p.Leu217Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154800 p.Trp438Gly missense_variant 1.0
katG 2154874 p.Tyr413Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyA 3074197 p.Pro92Arg missense_variant 0.11
thyA 3074588 c.-117A>G upstream_gene_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.99
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 0.99
ubiA 4269296 p.Met180Val missense_variant 0.97
ethA 4326116 p.Thr453Ile missense_variant 1.0
ethA 4326731 p.Ala248Asp missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0