TB-Profiler result

Run: SRR13861708
Summary

Run ID: SRR13861708

Sample name:

Date: 2024-10-04T13:26:43.226681

Number of reads: 1306226

Percentage reads mapped: 65.37

Median coverage: 44.0

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
dnaA 715 p.Thr239Pro missense_variant 1.0 isoniazid
fgd1 490955 p.Met58Arg missense_variant 1.0 pretomanid
delamanid
clofazimine
mshA 574818 c.-530G>C upstream_gene_variant 1.0 isoniazid
ethionamide
hadA 731861 c.-69G>C upstream_gene_variant 1.0 isoniazid
rpsL 781155 c.-405G>A upstream_gene_variant 1.0 streptomycin
fbiC 1304529 c.1599T>C synonymous_variant 1.0 pretomanid
delamanid
clofazimine
Rv1258c 1406845 p.Ala166Pro missense_variant 1.0 streptomycin
pyrazinamide
isoniazid
rrl 1476229 n.2572C>T non_coding_transcript_exon_variant 0.17 capreomycin Uncertain significance
linezolid
rrl 1476251 n.2594T>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476260 n.2603A>G non_coding_transcript_exon_variant 0.24 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476268 n.2611A>T non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476275 n.2618T>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476279 n.2622G>A non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid
rrl 1476280 n.2623A>C non_coding_transcript_exon_variant 0.23 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476293 n.2636C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476294 n.2637A>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476295 n.2638C>G non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476296 n.2639C>T non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476297 n.2640C>T non_coding_transcript_exon_variant 0.2 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476301 n.2644A>C non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476302 n.2645G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476311 n.2654G>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476312 n.2655T>C non_coding_transcript_exon_variant 0.22 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476313 n.2656G>A non_coding_transcript_exon_variant 0.21 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476332 n.2675G>C non_coding_transcript_exon_variant 0.29 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476353 n.2696G>T non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476372 n.2715T>C non_coding_transcript_exon_variant 0.35 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>A non_coding_transcript_exon_variant 0.26 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476428 n.2771C>T non_coding_transcript_exon_variant 0.32 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.37 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476481 n.2824T>C non_coding_transcript_exon_variant 0.28 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.16 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674607 p.Pro136Ser missense_variant 1.0 isoniazid
ethionamide
inhA 1674778 p.Pro193Ala missense_variant 1.0 isoniazid
ethionamide
rpsA 1833269 c.-273G>T upstream_gene_variant 1.0 pyrazinamide
bacA 2064115 p.Ala205Asp missense_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
PPE35 2169081 p.Leu511Ser missense_variant 1.0 pyrazinamide
PPE35 2169202 p.Ser471Pro missense_variant 1.0 pyrazinamide
Rv1979c 2222091 c.1074G>T synonymous_variant 1.0 bedaquiline
clofazimine
Rv1979c 2223306 c.-142T>A upstream_gene_variant 1.0 bedaquiline
clofazimine
pncA 2289228 p.Ile5Asn missense_variant 1.0 pyrazinamide
kasA 2518176 p.Ala21Gly missense_variant 1.0 isoniazid
eis 2714755 p.Pro193Gln missense_variant 1.0 kanamycin
amikacin
ahpC 2726324 c.132A>G synonymous_variant 1.0 isoniazid Not assoc w R - Interim
ahpC 2726362 p.Phe57Ser missense_variant 1.0 isoniazid
pepQ 2859580 p.Leu280Arg missense_variant 1.0 bedaquiline
clofazimine
pepQ 2859999 c.420G>T synonymous_variant 1.0 bedaquiline
clofazimine
Rv2681 2997338 c.600G>C synonymous_variant 1.0 capreomycin
thyX 3067940 c.6C>G synonymous_variant 1.0 para-aminosalicylic_acid
thyA 3074620 c.-149C>A upstream_gene_variant 1.0 para-aminosalicylic_acid
mtrB 3626051 p.Ser188Trp missense_variant 1.0 rifampicin
bedaquiline
ddn 3986889 p.Phe16Val missense_variant 1.0 pretomanid
delamanid
embC 4242041 p.Met727Leu missense_variant 1.0 ethambutol
embA 4244723 p.Gln497His missense_variant 1.0 ethambutol Uncertain significance
aftB 4267979 c.858G>C synonymous_variant 1.0 ethambutol