TB-Profiler result

Run: SRR27107246
Summary

Run ID: SRR27107246

Sample name:

Date: 08-02-2024 18:11:48

Number of reads: 2553590

Percentage reads mapped: 99.09

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.His445Tyr (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol
Pyrazinamide R pncA p.Pro62Arg (0.23)
Streptomycin R gid p.Tyr22* (1.00)
Fluoroquinolones R gyrA p.Asp94Tyr (0.91)
Moxifloxacin R gyrA p.Asp94Tyr (0.91)
Ofloxacin R gyrA p.Asp94Tyr (0.91)
Levofloxacin R gyrA p.Asp94Tyr (0.91)
Ciprofloxacin R gyrA p.Asp94Tyr (0.91)
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
lineage4.8 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.Asp94Tyr missense_variant 0.91 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761139 p.His445Tyr missense_variant 1.0 rifampicin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289057 p.Pro62Arg missense_variant 0.23 pyrazinamide
gid 4408137 p.Tyr22* stop_gained 1.0 streptomycin
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 760314 p.Val170Leu missense_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
fabG1 1673380 c.-60C>G upstream_gene_variant 0.17
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289071 p.His57Gln missense_variant 0.54
alr 3840764 c.657G>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.26
ethA 4326284 p.Leu397Pro missense_variant 1.0
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408232 c.-30C>T upstream_gene_variant 1.0