TB-Profiler result

Run: SRR25827438

Summary

Run ID: SRR25827438

Sample name:

Date: 02-02-2024 03:15:52

Number of reads: 9911430

Percentage reads mapped: 99.37

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.Ser450Leu (1.00)
Isoniazid R katG p.Ser315Thr (1.00)
Ethambutol R embB p.Met306Ile (0.99)
Pyrazinamide R pncA c.-11A>G (1.00)
Streptomycin
Fluoroquinolones R gyrA p.Asp94Tyr (0.99)
Moxifloxacin R gyrA p.Asp94Tyr (0.99)
Ofloxacin R gyrA p.Asp94Tyr (0.99)
Levofloxacin R gyrA p.Asp94Tyr (0.99)
Ciprofloxacin R gyrA p.Asp94Tyr (0.99)
Aminoglycosides R rrs n.1401A>G (1.00)
Amikacin R rrs n.1401A>G (1.00)
Capreomycin R rrs n.1401A>G (1.00)
Kanamycin R rrs n.1401A>G (1.00)
Cycloserine
Ethionamide R ethA c.385dupC (0.98), ethA c.385dupC (0.98)
Clofazimine
Para-aminosalicylic_acid
Delamanid
Bedaquiline
Linezolid R rplC p.Cys154Arg (0.99)
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.Asp94Tyr missense_variant 0.99 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin
rplC 801268 p.Cys154Arg missense_variant 0.99 linezolid
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 1.0 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid
pncA 2289252 c.-11A>G upstream_gene_variant 1.0 pyrazinamide
embB 4247431 p.Met306Ile missense_variant 0.99 ethambutol
ethA 4327088 c.385dupC frameshift_variant 0.98 ethionamide, ethionamide
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
fgd1 490671 c.-112A>G upstream_gene_variant 1.0
rpoC 766494 p.Gly1042Asp missense_variant 0.99
mmpL5 775639 p.Ile948Val missense_variant 1.0
mmpR5 779130 c.144dupC frameshift_variant 0.88
rpsL 781395 c.-165T>C upstream_gene_variant 1.0
Rv1258c 1406472 p.Thr290Ile missense_variant 0.99
rrs 1471659 n.-187C>T upstream_gene_variant 1.0
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 1.0
rrl 1475951 n.2294G>A non_coding_transcript_exon_variant 1.0
tlyA 1917972 c.33A>G synonymous_variant 1.0
PPE35 2168149 p.Pro822Ser missense_variant 1.0
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
folC 2747470 p.Ile43Ala missense_variant 0.98
ald 3087398 c.580dupG frameshift_variant 0.98
clpC1 4039729 p.Asp326Asn missense_variant 0.99
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4247028 p.Leu172Arg missense_variant 0.25
embB 4247033 p.Ser174Arg missense_variant 0.14
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
gid 4407973 p.Val77Gly missense_variant 0.98