TB-Profiler result

Run: SRR13861614

Summary

Run ID: SRR13861614

Sample name:

Date: 2024-04-15T07:53:01.192745

Number of reads: 2393470

Percentage reads mapped: 47.92

Median coverage: 81.0

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 377 p.Thr126Asn missense_variant 1.0 isoniazid
dnaA 1519 p.Arg507Ser missense_variant 1.0 isoniazid
gyrB 5709 p.Gly157Val missense_variant 1.0 levofloxacin
moxifloxacin
gyrA 9028 p.Val576Ala missense_variant 1.0 levofloxacin
moxifloxacin
Rv0565c 657669 c.-199C>A upstream_gene_variant 1.0 ethionamide
rpoB 762011 c.2205G>C synonymous_variant 1.0 rifampicin Not assoc w R - Interim
rpoB 762279 c.2474delA frameshift_variant 1.0 rifampicin
mmpS5 778823 p.Ile28Thr missense_variant 1.0 clofazimine
bedaquiline
rplC 800279 c.-530A>C upstream_gene_variant 1.0 linezolid
fbiC 1304640 c.1710A>C synonymous_variant 1.0 clofazimine
pretomanid
delamanid
Rv1258c 1406376 p.Gly322Val missense_variant 1.0 streptomycin
isoniazid
pyrazinamide
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.31 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.36 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.41 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.44 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.43 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.43 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.42 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.42 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.41 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.37 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.37 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 0.34 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.14 capreomycin Not assoc w R
linezolid Uncertain significance
PPE35 2169882 p.Ser244Ile missense_variant 0.99 pyrazinamide
eis 2714940 c.392delA frameshift_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
Rv2477c 2782900 c.1143C>G synonymous_variant 1.0 ethambutol
moxifloxacin
streptomycin
levofloxacin
kanamycin
rifampicin
amikacin
ald 3087311 c.492C>G synonymous_variant 1.0 cycloserine
Rv3236c 3613629 c.-513C>G upstream_gene_variant 1.0 pyrazinamide
fbiB 3642465 p.Asp311His missense_variant 1.0 clofazimine
pretomanid
delamanid
alr 3840300 p.Pro374His missense_variant 1.0 cycloserine
rpoA 3878288 p.Thr74Pro missense_variant 1.0 rifampicin
clpC1 4039415 c.1289dupA frameshift_variant 1.0 pyrazinamide
clpC1 4040792 c.-88A>T upstream_gene_variant 1.0 pyrazinamide
embA 4243235 c.3G>T synonymous_variant 1.0 ethambutol