TB-Profiler result

Run: ERR4799572
Summary

Run ID: ERR4799572

Sample name:

Date: 20-10-2023 03:32:44

Number of reads: 2712840

Percentage reads mapped: 99.55

Strain: lineage4.4

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 katG p.Ser315Thr (1.00)
Ethambutol R embB p.Gly406Ser (1.00)
Pyrazinamide R pncA p.Leu120Arg (0.98)
Streptomycin R gid p.Lys144* (1.00)
Fluoroquinolones R gyrA p.Ala90Val (0.98)
Moxifloxacin R gyrA p.Ala90Val (0.98)
Ofloxacin R gyrA p.Ala90Val (0.98)
Levofloxacin R gyrA p.Ala90Val (0.98)
Ciprofloxacin R gyrA p.Ala90Val (0.98)
Aminoglycosides
Amikacin R eis c.-14C>T (0.98)
Capreomycin
Kanamycin R eis c.-14C>T (0.98)
Cycloserine
Ethionamide R ethA p.Trp45* (0.98)
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
lineage4.4 Euro-American S;T None 0.99
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288883 p.Leu120Arg missense_variant 0.98 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 0.98 kanamycin, amikacin
embB 4247729 p.Gly406Ser missense_variant 1.0 ethambutol
ethA 4327340 p.Trp45* stop_gained 0.98 ethionamide
gid 4407773 p.Lys144* stop_gained 1.0 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
rpoC 764724 p.Phe452Cys missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 778867 c.-387C>G upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416800 p.Ala183Val missense_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2170558 p.Ala19Pro missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2714523 p.His270Gln missense_variant 1.0
Rv2752c 3065232 c.951_959dupAATGTCGCG disruptive_inframe_insertion 1.0
Rv2752c 3065715 c.477T>C synonymous_variant 0.98
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
embA 4243324 p.Val31Ala missense_variant 1.0
embB 4247548 c.1035C>T synonymous_variant 1.0
aftB 4268928 c.-92C>T upstream_gene_variant 1.0
aftB 4269375 c.-539G>A upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0