TB-Profiler result

Run: SRR20958128
Summary

Run ID: SRR20958128

Sample name:

Date: 13-01-2024 18:24:26

Number of reads: 13358523

Percentage reads mapped: 99.88

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 0.47
lineage4.9 Euro-American (H37Rv-like) T1 None 0.56
lineage4.3.3 Euro-American (LAM) LAM;T RD115 0.45
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 0.43
gyrA 7585 p.Ser95Thr missense_variant 0.48
gyrA 8040 p.Gly247Ser missense_variant 0.4
gyrA 9304 p.Gly668Asp missense_variant 0.46
rpoB 761880 p.Ala692Thr missense_variant 0.47
rpoC 764995 c.1626C>G synonymous_variant 0.42
mmpL5 775639 p.Ile948Val missense_variant 0.5
rpsL 781395 c.-165T>C upstream_gene_variant 0.44
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rpsA 1834836 p.Met432Thr missense_variant 0.42
tlyA 1917972 c.33A>G synonymous_variant 0.44
katG 2154459 c.1653C>T synonymous_variant 0.54
Rv1979c 2223293 c.-129A>G upstream_gene_variant 0.48
kasA 2518919 p.Gly269Ser missense_variant 0.53
thyA 3073868 p.Thr202Ala missense_variant 0.52
ald 3086788 c.-32T>C upstream_gene_variant 0.47
fprA 3473996 c.-11_-10insA upstream_gene_variant 0.49
rpoA 3878614 c.-107A>C upstream_gene_variant 0.14
rpoA 3878619 c.-112A>C upstream_gene_variant 0.13
clpC1 4038287 c.2418C>T synonymous_variant 0.45
embA 4242643 c.-590C>T upstream_gene_variant 0.41
embB 4247028 p.Leu172Arg missense_variant 0.21
whiB6 4338593 c.-73delT upstream_gene_variant 0.47
whiB6 4338596 c.-75G>C upstream_gene_variant 0.47
gid 4407720 c.483C>G synonymous_variant 0.51
gid 4408156 p.Leu16Arg missense_variant 0.42