TB-Profiler result

Run: SRR21798451
Summary

Run ID: SRR21798451

Sample name:

Date: 03-02-2024 02:13:44

Number of reads: 1281101

Percentage reads mapped: 99.69

Strain: lineage4.8;lineage4.7

Drug-resistance: Pre-XDR-TB

Download CSV Download TXT Download PDF Download JSON
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations
Rifampicin R rpoB p.Asp435Val (0.42)
Isoniazid R katG p.Ser315Thr (0.54)
Ethambutol R embA c.-16C>T (0.41), embB p.Met306Ile (0.48)
Pyrazinamide R pncA p.Leu182Trp (0.46)
Streptomycin R rrs n.513C>T (0.54)
Fluoroquinolones R gyrA p.Asp94Gly (0.46)
Moxifloxacin R gyrA p.Asp94Gly (0.46)
Ofloxacin R gyrA p.Asp94Gly (0.46)
Levofloxacin R gyrA p.Asp94Gly (0.46)
Ciprofloxacin R gyrA p.Asp94Gly (0.46)
Aminoglycosides R rrs n.1401A>G (0.62)
Amikacin R rrs n.1401A>G (0.62)
Capreomycin R rrs n.1401A>G (0.62)
Kanamycin R rrs n.1401A>G (0.62)
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
lineage4.7 Euro-American (mainly T) T1;T5 None 0.48
lineage4.8 Euro-American (mainly T) T1;T2;T3;T5 RD219 0.56
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 7582 p.Asp94Gly missense_variant 0.46 ofloxacin, moxifloxacin, levofloxacin, fluoroquinolones, ciprofloxacin
rpoB 761110 p.Asp435Val missense_variant 0.42 rifampicin
rrs 1472358 n.513C>T non_coding_transcript_exon_variant 0.54 streptomycin
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.62 kanamycin, capreomycin, aminoglycosides, amikacin
katG 2155168 p.Ser315Thr missense_variant 0.54 isoniazid
pncA 2288697 p.Leu182Trp missense_variant 0.46 pyrazinamide
embA 4243217 c.-16C>T upstream_gene_variant 0.41 ethambutol
embB 4247431 p.Met306Ile missense_variant 0.48 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 7246 c.-56T>C upstream_gene_variant 0.55
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
rrs 1472363 n.518G>A non_coding_transcript_exon_variant 0.57
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.58
rrl 1474963 n.1306G>T non_coding_transcript_exon_variant 0.59
tlyA 1917972 c.33A>G synonymous_variant 1.0
Rv1979c 2222321 p.Ile282Val missense_variant 0.57
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0
pncA 2289316 c.-75C>T upstream_gene_variant 0.5
fbiB 3641112 c.-423T>G upstream_gene_variant 0.49
alr 3840618 p.Asp268Gly missense_variant 0.37
embA 4242643 c.-590C>T upstream_gene_variant 1.0
embB 4249732 c.3219C>G synonymous_variant 0.86
whiB6 4338595 c.-75delG upstream_gene_variant 1.0
whiB6 4338706 c.-185C>T upstream_gene_variant 0.57
gid 4407964 p.Ala80Gly missense_variant 0.38