TB-Profiler result

Run: ERR4830650
Summary

Run ID: ERR4830650

Sample name:

Date: 20-10-2023 00:54:40

Number of reads: 4607562

Percentage reads mapped: 99.48

Strain: lineage4.2.1

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.Gln429Leu (1.00), rpoB p.Asp435Tyr (1.00)
Isoniazid R katG p.Ser315Thr (1.00), ahpC c.-48G>A (1.00)
Ethambutol R embB p.Gly406Ala (1.00)
Pyrazinamide
Streptomycin R gid p.Pro75Arg (1.00)
Fluoroquinolones R gyrA p.Asp94Tyr (1.00)
Moxifloxacin R gyrA p.Asp94Tyr (1.00)
Ofloxacin R gyrA p.Asp94Tyr (1.00)
Levofloxacin R gyrA p.Asp94Tyr (1.00)
Ciprofloxacin R gyrA p.Asp94Tyr (1.00)
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
lineage4.2 Euro-American H;T;LAM None 1.0
lineage4.2.1 Euro-American (TUR) H3;H4 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
gyrA 7581 p.Asp94Tyr missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761092 p.Gln429Leu missense_variant 1.0 rifampicin
rpoB 761109 p.Asp435Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
ahpC 2726145 c.-48G>A upstream_gene_variant 1.0 isoniazid
embB 4247730 p.Gly406Ala missense_variant 1.0 ethambutol
gid 4407979 p.Pro75Arg 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
gyrA 7362 p.Glu21Gln missense_variant 1.0
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834185 p.Val215Gly missense_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2167683 c.2926_2929delAACC frameshift_variant 1.0
PPE35 2169879 p.Phe245Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086742 c.-78A>C 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
embB 4249594 c.3081G>A synonymous_variant 1.0
ethA 4326843 p.Tyr211Asp missense_variant 1.0
ethA 4328376 c.-903G>C upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408411 c.-209G>A upstream_gene_variant 1.0