TB-Profiler result

Run: SRR8651642

Summary

Run ID: SRR8651642

Sample name:

Date: 21-10-2023 13:00:04

Number of reads: 1382514

Percentage reads mapped: 98.01

Strain: lineage4.5

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.Asp435Val (1.00)
Isoniazid R katG c.2044_2045insT (0.98), ahpC c.-81C>T (1.00)
Ethambutol
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrB p.Asp461His (1.00)
Moxifloxacin R gyrB p.Asp461His (1.00)
Ofloxacin R gyrB p.Asp461His (1.00)
Levofloxacin R gyrB p.Asp461His (1.00)
Ciprofloxacin R gyrB p.Asp461His (1.00)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R ethA c.1299dupG (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
lineage4.5 Euro-American H;T RD122 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
gyrB 6620 p.Asp461His missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
katG 2154067 c.2044_2045insT frameshift_variant 0.98 isoniazid
ahpC 2726112 c.-81C>T upstream_gene_variant 1.0 isoniazid
ethA 4326174 c.1299dupG frameshift_variant 1.0 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 7774 p.Gly158Val missense_variant 0.44
gyrA 7892 c.591G>A synonymous_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 575726 p.Thr127Pro missense_variant 1.0
mshA 575729 p.Gln128Met missense_variant 0.98
ccsA 620029 c.139C>T synonymous_variant 1.0
rpoC 764452 c.1083T>C synonymous_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776157 p.Asp775Gly missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416613 c.734dupC frameshift_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918226 p.Phe96Ser missense_variant 1.0
PPE35 2170568 p.Ile15Met missense_variant 1.0
Rv1979c 2221919 p.Val416Met missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288925 p.Phe106Cys missense_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
rpoA 3878575 c.-68C>T upstream_gene_variant 1.0
clpC1 4038318 p.Pro796Leu missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246163 c.-351G>A upstream_gene_variant 1.0
embB 4247723 p.Pro404Thr missense_variant 1.0
ubiA 4269671 p.Val55Leu missense_variant 1.0
whiB6 4338421 c.100delT frameshift_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408217 c.-15C>T upstream_gene_variant 1.0