TB-Profiler result

Run: SRR28393947
Summary

Run ID: SRR28393947

Sample name:

Date: 2024-05-22T08:23:16.225136

Number of reads: 13263650

Percentage reads mapped: 99.66

Median coverage: 415.0

Strain: lineage4

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 Euro-American None 1.0
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
isoniazid katG p.Tyr337Phe Mutation from literature
p.Tyr337Cys Uncertain significance Mutation from literature
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA c.417dupG Assoc w R
streptomycin
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
eis c.-8C>A Uncertain significance Mutation from literature
cycloserine
ethionamide ethA c.754_755dupGC Assoc w R
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 0.82 moxifloxacin Assoc w R High-level resistance
levofloxacin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.17 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
katG 2155102 p.Tyr337Phe missense_variant 0.35 isoniazid Mutation from literature
katG 2155102 p.Tyr337Cys missense_variant 0.65 isoniazid Uncertain significance Mutation from literature
pncA 2288824 c.417dupG frameshift_variant 1.0 pyrazinamide Assoc w R
eis 2715340 c.-8C>A upstream_gene_variant 0.85 kanamycin Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol Assoc w R
ethA 4326718 c.754_755dupGC frameshift_variant 0.14 ethionamide 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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rpoB 761889 p.Val695Leu missense_variant 1.0 rifampicin Uncertain significance
rpoC 764817 p.Val483Gly missense_variant 1.0 rifampicin Uncertain significance
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
rplC 801009 c.201A>G synonymous_variant 1.0 linezolid Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
PPE35 2168776 p.Pro613Thr missense_variant 0.83 pyrazinamide Uncertain significance
Rv1979c 2223214 c.-50A>C upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv2752c 3065517 c.675C>T synonymous_variant 1.0 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
Rv2752c 3065692 p.His167Arg missense_variant 1.0 ethambutol Uncertain significance
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
thyX 3068021 c.-76C>A upstream_gene_variant 0.83 para-aminosalicylic_acid
Rv3083 3448439 c.-64delA upstream_gene_variant 1.0 ethionamide
rpoA 3877947 c.561C>A synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoA 3878595 c.-88C>T upstream_gene_variant 0.27 rifampicin
rpoA 3878635 c.-128C>T upstream_gene_variant 0.23 rifampicin
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
ubiA 4269308 p.Phe176Leu missense_variant 0.15 ethambutol Uncertain significance
ethA 4326800 p.Leu225Pro missense_variant 0.87 ethionamide Uncertain significance
ethA 4328317 c.-844C>T upstream_gene_variant 1.0 ethionamide
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 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin