TB-Profiler result

Run: SRR23862027
Summary

Run ID: SRR23862027

Sample name:

Date: 12-04-2023 15:22:44

Number of reads: 3442628

Percentage reads mapped: 99.67

Strain: lineage4.8

Drug-resistance: MDR-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), inhA p.Ile194Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide R pncA p.His51Arg (1.00)
Streptomycin
Fluoroquinolones
Moxifloxacin
Ofloxacin
Levofloxacin
Ciprofloxacin
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (1.00), inhA p.Ile194Thr (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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
inhA 1674782 p.Ile194Thr missense_variant 1.0 isoniazid, ethionamide
pncA 2289090 p.His51Arg missense_variant 1.0 pyrazinamide
embB 4247429 p.Met306Val 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
rpoB 759945 p.Leu47Val missense_variant 0.79
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
ndh 2102989 c.54G>T synonymous_variant 1.0
katG 2155437 p.Met225Ile missense_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.99
PPE35 2168326 p.Asp763Tyr missense_variant 1.0
PPE35 2169902 p.Leu237Phe missense_variant 0.16
PPE35 2169910 p.Asn235Tyr missense_variant 0.17
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
thyX 3067868 c.78C>T synonymous_variant 1.0
rpoA 3878641 c.-134C>G upstream_gene_variant 0.36
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247024 p.Pro171Ala missense_variant 0.25
ethR 4328030 p.Ala161Gly missense_variant 0.33
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407727 p.Met159Arg missense_variant 1.0
gid 4408127 p.Leu26Val missense_variant 1.0
gid 4408210 c.-8A>C upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0