TB-Profiler result

Run: SRR25827751
Summary

Run ID: SRR25827751

Sample name:

Date: 02-02-2024 18:11:18

Number of reads: 4751263

Percentage reads mapped: 99.15

Strain: lineage4.3.3

Drug-resistance: Pre-XDR-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.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.88), embB p.Asp1024Asn (0.93)
Pyrazinamide R pncA p.Gly97Asp (0.90)
Streptomycin R gid p.Leu79Ser (0.84)
Fluoroquinolones R gyrA p.Ala90Val (1.00)
Moxifloxacin R gyrA p.Ala90Val (1.00)
Ofloxacin R gyrA p.Ala90Val (1.00)
Levofloxacin R gyrA p.Ala90Val (1.00)
Ciprofloxacin R gyrA p.Ala90Val (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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.9
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.9
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 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2288952 p.Gly97Asp missense_variant 0.9 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.88 ethambutol
embB 4249583 p.Asp1024Asn missense_variant 0.93 ethambutol
gid 4407967 p.Leu79Ser missense_variant 0.84 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 8040 p.Gly247Ser missense_variant 0.9
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.88
rpoC 766487 p.Pro1040Ala missense_variant 0.91
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 0.86
rpsA 1834836 p.Met432Thr missense_variant 0.9
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.87
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 0.86
eis 2715152 p.Met61Val missense_variant 0.86
ahpC 2726080 c.-113G>A upstream_gene_variant 0.91
folC 2746340 p.Ala420Val missense_variant 0.92
thyA 3073679 c.792_*1insT frameshift_variant&splice_region_variant 0.87
thyA 3073868 p.Thr202Ala missense_variant 0.83
ald 3086788 c.-32T>C upstream_gene_variant 0.99
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.88
clpC1 4038968 c.1737G>A synonymous_variant 0.9
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4245835 p.Leu868Arg missense_variant 0.21
embB 4247015 p.Ser168Ala missense_variant 0.28
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407588 c.615A>G synonymous_variant 0.15
gid 4407927 p.Glu92Asp missense_variant 0.15
gid 4408156 p.Leu16Arg missense_variant 0.88