TB-Profiler result

Run: SRR1166100
Summary

Run ID: SRR1166100

Sample name:

Date: 21-10-2023 10:33:29

Number of reads: 10163715

Percentage reads mapped: 99.63

Strain: lineage4.8

Drug-resistance: RR-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 (1.00)
Isoniazid
Ethambutol R embA c.-16C>T (1.00), embB p.Asp354Ala (1.00)
Pyrazinamide R pncA c.-52_*1649del (1.00)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
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
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247574 p.Asp354Ala missense_variant 1.0 ethambutol
pncA 2287031 c.-52_*1649del transcript_ablation 1.0 pyrazinamide
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
mshA 575891 p.Ala182Thr missense_variant 1.0
mshA 576313 c.968_972dupCACGG frameshift_variant 0.96
rpoB 761591 p.Asp595Glu missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpL5 776409 p.Leu691Arg missense_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155819 p.Tyr98Cys missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3064799 p.Arg465Trp missense_variant 1.0
rpoA 3877918 p.Glu197Gly missense_variant 0.18
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embA 4242928 c.-305A>G upstream_gene_variant 1.0
embB 4247595 p.Cys361Ser missense_variant 1.0
aftB 4268040 p.Leu266Pro missense_variant 1.0
whiB6 4338334 c.186_187delTG frameshift_variant 0.32
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0