TB-Profiler result

Run: SRR13861155
Summary

Run ID: SRR13861155

Sample name:

Date: 2024-10-04T18:09:52.796247

Number of reads: 1213358

Percentage reads mapped: 40.49

Median coverage: 41.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

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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
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
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 6561 p.Lys441Arg missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 7705 p.Thr135Ser missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 8409 p.Leu370Ile missense_variant 1.0 levofloxacin
moxifloxacin
Rv0010c 13327 p.Leu78Ile missense_variant 1.0 isoniazid
ccsA 619637 c.-254T>G upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
ccsA 620157 c.267G>T synonymous_variant 1.0 kanamycin
capreomycin
amikacin
rplC 801215 c.408delC frameshift_variant 1.0 linezolid
Rv1129c 1253639 p.Leu299* stop_gained 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
fbiC 1304409 c.1479C>G synonymous_variant 1.0 pretomanid
delamanid
clofazimine
fbiC 1304501 p.Ala524Gly missense_variant 1.0 pretomanid
delamanid Uncertain significance
clofazimine Uncertain significance
sigE 1365081 c.669G>T synonymous_variant 1.0 pyrazinamide
rrs 1472791 n.946G>C non_coding_transcript_exon_variant 1.0 kanamycin Uncertain significance
capreomycin
streptomycin
amikacin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.29 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.39 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.38 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.35 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.35 capreomycin Not assoc w R
linezolid Uncertain significance
PPE35 2168564 c.2049T>A synonymous_variant 1.0 pyrazinamide
kasA 2519179 c.1065G>C synonymous_variant 1.0 isoniazid
folC 2746546 p.Asp351Glu missense_variant 1.0 para-aminosalicylic_acid
Rv2477c 2784407 c.-365A>G upstream_gene_variant 1.0 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2680 2996063 c.-42G>C upstream_gene_variant 1.0 capreomycin
thyX 3068038 c.-93C>A upstream_gene_variant 1.0 para-aminosalicylic_acid
Rv3083 3448608 c.105G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
whiB7 3569032 c.-353C>A upstream_gene_variant 1.0 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612721 c.396G>T synonymous_variant 1.0 pyrazinamide
fbiA 3641221 p.Pro227Ala missense_variant 1.0 pretomanid
delamanid
clofazimine
rpoA 3879230 c.-723C>G upstream_gene_variant 1.0 rifampicin
clpC1 4039647 p.Glu353Ala missense_variant 1.0 pyrazinamide
clpC1 4040955 c.-251A>C upstream_gene_variant 1.0 pyrazinamide
embC 4239484 c.-379T>C upstream_gene_variant 1.0 ethambutol
embC 4240006 c.144A>C synonymous_variant 1.0 ethambutol
embA 4244074 p.Ala281Val missense_variant 1.0 ethambutol
embA 4245739 p.Arg836His missense_variant 1.0 ethambutol
ethA 4326731 p.Ala248Gly missense_variant 1.0 ethionamide
ethR 4327623 c.75_76insC frameshift_variant 1.0 ethionamide Uncertain significance
gid 4408334 c.-132G>T upstream_gene_variant 1.0 streptomycin