TB-Profiler result

Run: SRR20958123
Summary

Run ID: SRR20958123

Sample name:

Date: 03-02-2024 10:17:12

Number of reads: 19292199

Percentage reads mapped: 99.77

Strain: lineage4.9;lineage4.3.3

Drug-resistance: Sensitive

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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
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
lineage4.3 Euro-American (LAM) mainly-LAM None 0.95
lineage4.9 Euro-American (H37Rv-like) T1 None 0.05
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.94
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
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 0.94
gyrA 7585 p.Ser95Thr missense_variant 0.96
gyrA 8040 p.Gly247Ser missense_variant 0.96
gyrA 9304 p.Gly668Asp missense_variant 0.94
rpoB 761880 p.Ala692Thr missense_variant 0.95
rpoC 764995 c.1626C>G synonymous_variant 0.94
mmpL5 775639 p.Ile948Val missense_variant 0.96
rpsL 781395 c.-165T>C upstream_gene_variant 0.96
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.95
tlyA 1917972 c.33A>G synonymous_variant 0.95
tlyA 1918596 c.657C>T synonymous_variant 0.93
katG 2154459 c.1653C>T synonymous_variant 0.94
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.95
kasA 2518919 p.Gly269Ser missense_variant 0.96
thyA 3073868 p.Thr202Ala missense_variant 0.95
ald 3086788 c.-32T>C upstream_gene_variant 0.96
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.95
clpC1 4038287 c.2418C>T synonymous_variant 0.93
embA 4242643 c.-590C>T upstream_gene_variant 0.95
embB 4247028 p.Leu172Arg missense_variant 0.18
embB 4247039 p.Phe176Val missense_variant 0.11
whiB6 4338595 c.-75delG upstream_gene_variant 0.93
gid 4407720 c.483C>G synonymous_variant 0.93
gid 4408156 p.Leu16Arg missense_variant 0.95