TB-Profiler result

Run: ERR4809241

Summary

Run ID: ERR4809241

Sample name:

Date: 20-10-2023 14:36:28

Number of reads: 4302296

Percentage reads mapped: 99.56

Strain: lineage4.2.1;lineage4.1.2

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 (0.84)
Isoniazid R katG p.Ser315Thr (0.85)
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
lineage4.1 Euro-American T;X;H None 0.13
lineage4.2 Euro-American H;T;LAM None 0.87
lineage4.1.2 Euro-American T;H None 0.1
lineage4.2.1 Euro-American (TUR) H3;H4 None 0.89
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 0.84 rifampicin
katG 2155168 p.Ser315Thr missense_variant 0.85 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 9304 p.Gly668Asp missense_variant 1.0
fgd1 491238 c.456C>T synonymous_variant 0.88
fgd1 491247 c.465C>T synonymous_variant 0.9
fgd1 491591 p.Lys270Met missense_variant 0.12
rpoB 760115 c.309C>T synonymous_variant 0.12
rpoC 764123 p.Phe252Leu missense_variant 0.87
rpoC 764263 c.894G>A synonymous_variant 0.18
rpoC 764817 p.Val483Ala missense_variant 0.78
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777320 c.1161C>G synonymous_variant 0.16
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 0.99
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 0.9
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
kasA 2518773 p.Asn220Ser missense_variant 0.86
ald 3086742 c.-78A>C upstream_gene_variant 0.9
ald 3086788 c.-32T>C upstream_gene_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
Rv3236c 3611974 c.1143A>C synonymous_variant 0.13
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embC 4242803 p.Val981Leu missense_variant 0.2
embA 4243218 c.-15C>G upstream_gene_variant 0.82
embB 4249594 c.3081G>A synonymous_variant 0.89
ethA 4328376 c.-903G>C upstream_gene_variant 0.89
whiB6 4338595 c.-75delG upstream_gene_variant 1.0