TB-Profiler result

Run: SRR21798451
Summary

Run ID: SRR21798451

Sample name:

Date: 2024-04-16T06:40:15.336228

Number of reads: 1281101

Percentage reads mapped: 99.69

Median coverage: 43.0

Strain: lineage4.7;lineage4.8

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.7 Euro-American (mainly T) None 0.48
lineage4 Euro-American None 1.0
lineage4.8 Euro-American (mainly T) RD219 0.56
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Asp435Val Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Met306Ile Assoc w R
pyrazinamide pncA p.Leu182Trp Assoc w R
streptomycin rrs n.513C>T Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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 Confidence Comment
gyrA 7582 p.Asp94Gly missense_variant 0.46 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761110 p.Asp435Val missense_variant 0.42 rifampicin Assoc w R
rrs 1472358 n.513C>T non_coding_transcript_exon_variant 0.54 streptomycin Uncertain significance Mutation from literature
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.62 capreomycin Assoc w R
amikacin Assoc w R
kanamycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.54 isoniazid Assoc w R High-level resistance
pncA 2288697 p.Leu182Trp missense_variant 0.46 pyrazinamide Assoc w R
embA 4243217 c.-16C>T upstream_gene_variant 0.41 ethambutol Uncertain significance Mutation from literature
embB 4247431 p.Met306Ile missense_variant 0.48 ethambutol Assoc w R
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 Drugs Confidence
gyrB 7246 c.2007T>C synonymous_variant 0.55 levofloxacin Not assoc w R - Interim
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
sigE 1364685 c.273C>T synonymous_variant 0.58 pyrazinamide
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrs 1472363 n.518G>A non_coding_transcript_exon_variant 0.57 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474001 n.344C>T non_coding_transcript_exon_variant 0.58 capreomycin Not assoc w R
linezolid Not assoc w R
rrl 1474963 n.1306G>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2156631 c.-520T>C upstream_gene_variant 0.54 isoniazid Uncertain significance
Rv1979c 2222321 p.Ile282Val missense_variant 0.57 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289316 c.-75C>T upstream_gene_variant 0.5 pyrazinamide
fbiB 3641112 c.-423T>G upstream_gene_variant 0.49 clofazimine
pretomanid
delamanid
alr 3840618 p.Asp268Gly missense_variant 0.37 cycloserine
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embB 4249732 c.3219C>G synonymous_variant 0.86 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338706 c.-185C>T upstream_gene_variant 0.57 capreomycin
amikacin
kanamycin
gid 4407964 p.Ala80Gly missense_variant 0.38 streptomycin