TB-Profiler result

Run: ERR4799107
Summary

Run ID: ERR4799107

Sample name:

Date: 20-10-2023 03:29:18

Number of reads: 6464542

Percentage reads mapped: 99.69

Strain: lineage4.8

Drug-resistance: 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.His445Cys (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Val (1.00)
Pyrazinamide
Streptomycin R rpsL p.Lys43Arg (0.99)
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
Kanamycin
Cycloserine
Ethionamide
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.93)
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 0.99
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 761139 p.His445Cys missense_variant 1.0 rifampicin
rpsL 781687 p.Lys43Arg missense_variant 0.99 streptomycin
rplC 801268 p.Cys154Arg missense_variant 0.93 linezolid
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
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
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 0.96
tlyA 1917972 c.33A>G synonymous_variant 1.0
katG 2155824 c.288C>T synonymous_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2288742 p.Thr167Ile missense_variant 0.98
thyA 3074221 p.Ala84Glu missense_variant 0.96
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326450 p.Thr342Ala missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.98