TB-Profiler result

Run: SRR23861868
Summary

Run ID: SRR23861868

Sample name:

Date: 12-04-2023 07:50:25

Number of reads: 5422472

Percentage reads mapped: 99.78

Strain: lineage4.6.5

Drug-resistance: Other

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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol R embB p.Ala313Val (1.00)
Pyrazinamide
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin R tlyA p.Asn236Lys (1.00)
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
lineage4.6 Euro-American T;LAM None 1.0
lineage4.6.5 Euro-American T;LAM 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
tlyA 1918647 p.Asn236Lys missense_variant 1.0 capreomycin
embB 4247451 p.Ala313Val missense_variant 1.0 ethambutol
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 0.99
gyrA 7585 p.Ser95Thr missense_variant 1.0
gyrA 9304 p.Gly668Asp missense_variant 1.0
mshA 576106 c.759C>G synonymous_variant 0.14
mshA 576108 p.Ala254Gly missense_variant 0.14
rpoC 763443 p.Tyr25Cys missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 777974 c.507C>T synonymous_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
fbiC 1304451 c.1521C>T synonymous_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2154587 p.Asp509Asn missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2746995 p.Val202Ile missense_variant 1.0
pepQ 2859552 c.867C>T synonymous_variant 1.0
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0
whiB7 3568416 p.Lys88His missense_variant 0.18
whiB7 3568428 c.252A>C synonymous_variant 0.3
clpC1 4040235 p.Gly157Ala missense_variant 0.16
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4246574 p.Ala21Ser missense_variant 0.16
embB 4246993 p.Asn160Lys missense_variant 0.13
embB 4247013 p.Pro167Arg missense_variant 0.2
embB 4247028 p.Leu172Arg missense_variant 0.16
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407914 p.Arg97Cys missense_variant 1.0