TB-Profiler result

Run: ERR4799768

Summary

Run ID: ERR4799768

Sample name:

Date: 20-10-2023 04:09:51

Number of reads: 2597752

Percentage reads mapped: 99.63

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.Ser450Leu (1.00)
Isoniazid R fabG1 c.-15C>T (0.96), katG p.Ser315Thr (0.94)
Ethambutol R embB p.Met306Val (0.60), embB p.Gly406Asp (0.11), embB p.Gln497Arg (0.29)
Pyrazinamide
Streptomycin
Fluoroquinolones R gyrA p.Ser91Pro (0.22), gyrA p.Asp94Gly (0.49)
Moxifloxacin R gyrA p.Ser91Pro (0.22), gyrA p.Asp94Gly (0.49)
Ofloxacin R gyrA p.Ser91Pro (0.22), gyrA p.Asp94Gly (0.49)
Levofloxacin R gyrA p.Ser91Pro (0.22), gyrA p.Asp94Gly (0.49)
Ciprofloxacin R gyrA p.Ser91Pro (0.22), gyrA p.Asp94Gly (0.49)
Aminoglycosides
Amikacin
Capreomycin
Kanamycin
Cycloserine
Ethionamide R fabG1 c.-15C>T (0.96)
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 0.98
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 7572 p.Ser91Pro missense_variant 0.22 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
gyrA 7582 p.Asp94Gly missense_variant 0.49 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
fabG1 1673425 c.-15C>T upstream_gene_variant 0.96 isoniazid, ethionamide
katG 2155168 p.Ser315Thr missense_variant 0.94 isoniazid
embB 4247429 p.Met306Val missense_variant 0.6 ethambutol
embB 4247730 p.Gly406Asp missense_variant 0.11 ethambutol
embB 4248003 p.Gln497Arg missense_variant 0.29 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 0.98
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 0.98
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
clpC1 4039729 p.Asp326Asn missense_variant 0.97
embA 4242643 c.-590C>T upstream_gene_variant 1.0
ethA 4326632 p.His281Arg missense_variant 0.99
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4408094 p.Gly37Arg missense_variant 0.97
Rv3083 3448507 c.5_*1408del frameshift_variant&stop_lost&splice_region_variant 0.99