TB-Profiler result

Run: ERR2184306

Summary

Run ID: ERR2184306

Sample name:

Date: 20-10-2023 05:55:56

Number of reads: 3054240

Percentage reads mapped: 99.57

Strain: lineage4.1.1

Drug-resistance: MDR-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 fabG1 c.-8T>G (1.00), katG p.Ser315Thr (1.00)
Ethambutol R embA c.-11C>A (1.00), embB p.Met306Val (1.00)
Pyrazinamide R pncA p.Ser18* (1.00)
Streptomycin R gid p.Leu108Arg (1.00)
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin R eis c.-14C>T (1.00)
Capreomycin
Kanamycin R eis c.-14C>T (1.00)
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
lineage4.1 Euro-American T;X;H None 1.0
lineage4.1.1 Euro-American (X-type) X1;X2;X3 None 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673432 c.-8T>G upstream_gene_variant 1.0 isoniazid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289189 p.Ser18* stop_gained 1.0 pyrazinamide
eis 2715346 c.-14C>T upstream_gene_variant 1.0 kanamycin, amikacin
embA 4243222 c.-11C>A upstream_gene_variant 1.0 ethambutol
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol
gid 4407880 p.Leu108Arg missense_variant 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
gyrB 6052 p.Ile271Met missense_variant 1.0
gyrB 7221 p.Ser661Thr missense_variant 1.0
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 765150 p.Gly594Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416699 p.Leu217Val missense_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
eis 2715266 p.Ser23Arg missense_variant 0.57
thyX 3067948 c.-3G>A upstream_gene_variant 1.0
thyA 3074336 p.Thr46Pro missense_variant 1.0
thyA 3074588 c.-117A>G upstream_gene_variant 1.0
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
embC 4242803 p.Val981Leu missense_variant 1.0
embB 4249408 c.2895G>A synonymous_variant 1.0
ethA 4326116 p.Thr453Ile missense_variant 1.0
ethA 4327314 p.Arg54Cys missense_variant 1.0
whiB6 4337828 c.-2060_*342del transcript_ablation 1.0
whiB6 4337829 c.-2060_*341del transcript_ablation 1.0