TB-Profiler result

Run: SRR5551667
Summary

Run ID: SRR5551667

Sample name:

Date: 20-10-2023 17:19:38

Number of reads: 1266384

Percentage reads mapped: 99.67

Strain: lineage4.8

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.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol R embA c.-16C>T (1.00), embB p.Asp328Val (1.00)
Pyrazinamide R pncA c.47dupG (1.00), pncA c.47dupG (1.00)
Streptomycin R rpsL p.Lys43Arg (1.00)
Fluoroquinolones R gyrA p.Asp94His (1.00)
Moxifloxacin R gyrA p.Asp94His (1.00)
Ofloxacin R gyrA p.Asp94His (1.00)
Levofloxacin R gyrA p.Asp94His (1.00)
Ciprofloxacin R gyrA p.Asp94His (1.00)
Aminoglycosides
Amikacin
Capreomycin R tlyA c.39dupG (0.17), tlyA c.271_272dupGC (0.19)
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00)
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
gyrA 7581 p.Asp94His missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
tlyA 1917976 c.39dupG frameshift_variant 0.17 capreomycin
tlyA 1918207 c.271_272dupGC frameshift_variant 0.19 capreomycin
pncA 2289194 c.47dupG frameshift_variant 1.0 pyrazinamide, pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 1.0 ethambutol
embB 4247496 p.Asp328Val 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 1.0
rpoC 763328 c.-42_-41insT upstream_gene_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
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
tlyA 1918478 p.Leu180Arg missense_variant 0.54
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
ald 3086906 c.89dupG frameshift_variant 0.22
ald 3087095 c.276C>T synonymous_variant 1.0
ddn 3986911 p.Arg23Gln missense_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0