TB-Profiler result

Run: ERR4813211
Summary

Run ID: ERR4813211

Sample name:

Date: 20-10-2023 05:09:11

Number of reads: 3398601

Percentage reads mapped: 99.72

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.Ser450Trp (1.00)
Isoniazid R fabG1 c.-15C>T (1.00)
Ethambutol R embB p.Gln497Arg (1.00)
Pyrazinamide R pncA c.412delT (1.00)
Streptomycin R gid p.Gln127* (1.00)
Fluoroquinolones R gyrB p.Ala504Val (1.00), gyrA p.Asp94Ala (1.00)
Moxifloxacin R gyrB p.Ala504Val (1.00), gyrA p.Asp94Ala (1.00)
Ofloxacin R gyrB p.Ala504Val (1.00), gyrA p.Asp94Ala (1.00)
Levofloxacin R gyrB p.Ala504Val (1.00), gyrA p.Asp94Ala (1.00)
Ciprofloxacin R gyrB p.Ala504Val (1.00), gyrA p.Asp94Ala (1.00)
Aminoglycosides
Amikacin
Capreomycin R tlyA c.397dupC (1.00), tlyA c.397dupC (1.00)
Kanamycin
Cycloserine R alr p.Met343Thr (0.94)
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
gyrB 6750 p.Ala504Val missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Ala missense_variant 1.0 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Trp missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid, ethionamide
tlyA 1918335 c.397dupC frameshift_variant 1.0 capreomycin, capreomycin
pncA 2288829 c.412delT frameshift_variant 1.0 pyrazinamide
alr 3840393 p.Met343Thr missense_variant 0.94 cycloserine
embB 4248003 p.Gln497Arg missense_variant 1.0 ethambutol
gid 4407824 p.Gln127* 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 762303 p.Val833Met missense_variant 1.0
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpS5 779588 c.-683C>T upstream_gene_variant 1.0
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
embR 1416914 p.Trp145Ser missense_variant 0.21
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 2155565 p.Phe183Leu missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
Rv2752c 3065926 p.Ala89Glu missense_variant 1.0
ald 3087091 c.273delG frameshift_variant 1.0
alr 3840764 c.657G>C synonymous_variant 1.0
embA 4242643 c.-590C>T upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 1.0