TB-Profiler result

Run: SRR13837551
Summary

Run ID: SRR13837551

Sample name:

Date: 2024-10-04T05:49:38.743746

Number of reads: 589648

Percentage reads mapped: 97.34

Median coverage: 20.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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
lineage4.9 Euro-American (H37Rv-like) 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
isoniazid
ethambutol
pyrazinamide
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid fgd1 p.Lys259* Assoc w R - Interim Confers DLM-PMD cross-resistance
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
fgd1 491557 p.Lys259* stop_gained 1.0 delamanid Assoc w R - Interim Confers DLM-PMD cross-resistance
pretomanid Assoc w R - Interim Confers DLM-PMD cross-resistance
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
dnaA 1509 p.Gln503His missense_variant 1.0 isoniazid Uncertain significance
gyrB 5417 p.Gly60Ser missense_variant 1.0 levofloxacin
moxifloxacin
gyrB 6381 p.Lys381Arg missense_variant 1.0 levofloxacin
moxifloxacin
fgd1 491364 c.582T>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
Rv0565c 657034 p.Tyr146Cys missense_variant 1.0 ethionamide Uncertain significance
rpoB 759579 c.-228G>A upstream_gene_variant 1.0 rifampicin
sigE 1364881 p.Glu157Lys missense_variant 1.0 pyrazinamide
Rv1258c 1406579 c.762C>T synonymous_variant 1.0 streptomycin
pyrazinamide
isoniazid
rrl 1473445 n.-213G>T upstream_gene_variant 1.0 capreomycin
linezolid
rrl 1475387 n.1730C>T non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
inhA 1673735 c.-467G>T upstream_gene_variant 0.97 isoniazid
ethionamide
inhA 1674246 c.45C>T synonymous_variant 1.0 isoniazid
ethionamide
inhA 1674937 c.736C>T synonymous_variant 1.0 isoniazid
ethionamide
rpsA 1833345 c.-196delC upstream_gene_variant 1.0 pyrazinamide
tsnR 1853672 c.70delG frameshift_variant 1.0 linezolid Uncertain significance
PPE35 2170775 c.-163T>A upstream_gene_variant 1.0 pyrazinamide
pncA 2289663 c.-422A>G upstream_gene_variant 1.0 pyrazinamide
pncA 2290143 c.-903_-902insG upstream_gene_variant 1.0 pyrazinamide
eis 2714984 p.Ala117Thr missense_variant 1.0 kanamycin
amikacin
ahpC 2726534 c.342C>T synonymous_variant 1.0 isoniazid
thyA 3074240 p.Thr78Ser missense_variant 1.0 para-aminosalicylic_acid
ald 3086806 c.-14_-13insA upstream_gene_variant 1.0 cycloserine
Rv3083 3448862 p.Gly120Ala missense_variant 1.0 ethionamide
alr 3840667 p.Arg252Gly missense_variant 1.0 cycloserine
rpoA 3878142 c.366C>G synonymous_variant 1.0 rifampicin
clpC1 4040117 p.Glu196Asp missense_variant 0.94 pyrazinamide
embA 4242988 c.-245A>G upstream_gene_variant 1.0 ethambutol
ubiA 4269624 p.Tyr70* stop_gained 1.0 ethambutol
ethR 4328039 p.Arg164Pro missense_variant 1.0 ethionamide
whiB6 4338235 p.Arg96Leu missense_variant 1.0 kanamycin
capreomycin
amikacin