TB-Profiler result

Run: ERR2184621

Summary

Run ID: ERR2184621

Sample name:

Date: 20-10-2023 06:22:45

Number of reads: 2961785

Percentage reads mapped: 99.67

Strain: lineage4.8

Drug-resistance: Other


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Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin
Isoniazid
Ethambutol
Pyrazinamide
Streptomycin
Fluoroquinolones R gyrB p.Arg446Cys (0.15), gyrA p.Ser91Pro (0.66)
Moxifloxacin R gyrB p.Arg446Cys (0.15), gyrA p.Ser91Pro (0.66)
Ofloxacin R gyrB p.Arg446Cys (0.15), gyrA p.Ser91Pro (0.66)
Levofloxacin R gyrB p.Arg446Cys (0.15), gyrA p.Ser91Pro (0.66)
Ciprofloxacin R gyrB p.Arg446Cys (0.15), gyrA p.Ser91Pro (0.66)
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 0.95
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 6575 p.Arg446Cys missense_variant 0.15 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7572 p.Ser91Pro missense_variant 0.66 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
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
gyrA 9217 p.Asp639Gly missense_variant 0.94
rpoC 767302 c.3933C>T synonymous_variant 0.95
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 0.88
PPE35 2168149 p.Pro822Ser missense_variant 0.96
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pepQ 2860283 p.Phe46Leu missense_variant 0.93
clpC1 4039729 p.Asp326Asn missense_variant 0.97
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 0.95