TB-Profiler result

Run: ERR4830048

Summary

Run ID: ERR4830048

Sample name:

Date: 20-10-2023 01:36:52

Number of reads: 4429178

Percentage reads mapped: 99.55

Strain: lineage4.5;lineage4.3.3

Drug-resistance: HR-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
Isoniazid R katG p.Ser315Thr (0.15)
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
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
lineage4.5 Euro-American H;T RD122 0.89
lineage4.3 Euro-American (LAM) mainly-LAM None 0.08
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.11
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
katG 2155168 p.Ser315Thr missense_variant 0.15 isoniazid
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 7892 c.591G>A synonymous_variant 0.94
gyrA 9304 p.Gly668Asp missense_variant 1.0
ccsA 620029 c.139C>T synonymous_variant 0.92
rpoC 764995 c.1626C>G synonymous_variant 0.12
rpoC 766667 p.Ser1100Ala missense_variant 0.1
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406101 p.Pro414Ser missense_variant 0.92
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155087 p.Glu342Ala missense_variant 0.89
PPE35 2170568 p.Ile15Met missense_variant 0.91
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715271 p.Ala21Glu missense_variant 0.86
ald 3086788 c.-32T>C upstream_gene_variant 0.13
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 0.94
clpC1 4038287 c.2418C>T synonymous_variant 0.13
clpC1 4038318 p.Pro796Leu missense_variant 0.88
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4248316 c.1803C>T synonymous_variant 0.19
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408009 p.Val65Ala missense_variant 0.14
gid 4408156 p.Leu16Arg missense_variant 0.16