TB-Profiler result

Run: SRR6046680

Summary

Run ID: SRR6046680

Sample name:

Date: 20-10-2023 18:08:22

Number of reads: 2487519

Percentage reads mapped: 99.24

Strain: lineage4.3.3

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.His445Asp (1.00)
Isoniazid R fabG1 c.-15C>T (0.99), katG p.Ser315Thr (0.99)
Ethambutol R embA c.-12C>T (0.97), embB p.Gln497Arg (0.99)
Pyrazinamide R pncA p.Asp49Gly (0.99)
Streptomycin
Fluoroquinolones R gyrB p.Asn499Asp (0.99)
Moxifloxacin R gyrB p.Asn499Asp (0.99)
Ofloxacin R gyrB p.Asn499Asp (0.99)
Levofloxacin R gyrB p.Asn499Asp (0.99)
Ciprofloxacin R gyrB p.Asn499Asp (0.99)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin R eis c.-12C>T (1.00)
Cycloserine R alr p.Leu113Arg (0.98)
Ethionamide R fabG1 c.-15C>T (0.99), ethA c.668_671delAGAA (1.00), ethA c.668_671delAGAA (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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.99
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.98
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
gyrB 6734 p.Asn499Asp missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Asp missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.99 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid
pncA 2289096 p.Asp49Gly missense_variant 0.99 pyrazinamide
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin
alr 3841083 p.Leu113Arg missense_variant 0.98 cycloserine
embA 4243221 c.-12C>T upstream_gene_variant 0.97 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.99 ethambutol
ethA 4326802 c.668_671delAGAA 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 8040 p.Gly247Ser missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
rpoC 764995 c.1626C>G synonymous_variant 0.97
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1303095 c.165G>A synonymous_variant 1.0
fbiC 1304962 p.Trp678Gly missense_variant 0.98
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2156196 c.-85C>T upstream_gene_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518919 p.Gly269Ser missense_variant 1.0
folC 2746340 p.Ala420Val missense_variant 1.0
ribD 2986827 c.-12G>A upstream_gene_variant 1.0
thyA 3073868 p.Thr202Ala missense_variant 1.0
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
clpC1 4038287 c.2418C>T synonymous_variant 0.93
clpC1 4038968 c.1737G>A synonymous_variant 0.94
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408156 p.Leu16Arg missense_variant 1.0