TB-Profiler result

Run: SRR13861571
Summary

Run ID: SRR13861571

Sample name:

Date: 2024-10-05T07:38:16.050731

Number of reads: 366003

Percentage reads mapped: 9.16

Median coverage: 12.0

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
mshA 575194 c.-154G>T upstream_gene_variant 1.0 isoniazid
ethionamide
hadA 731960 p.His11Asp missense_variant 1.0 isoniazid
hadA 732111 p.Cys61Tyr missense_variant 1.0 isoniazid
mmaA3 737975 p.Leu59Val missense_variant 1.0 isoniazid
rpoB 760907 c.1101_1102insT frameshift_variant 0.92 rifampicin
rpoC 764387 c.1018T>C synonymous_variant 0.33 rifampicin Not assoc w R - Interim
rpoC 764405 c.1036A>C synonymous_variant 0.36 rifampicin Not assoc w R - Interim
rpoC 764434 c.1065A>G synonymous_variant 0.43 rifampicin Not assoc w R - Interim
Rv1129c 1254602 c.-68C>T upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
Rv1129c 1254678 c.-144A>G upstream_gene_variant 1.0 levofloxacin
moxifloxacin
isoniazid
rifampicin
sigE 1364750 p.Thr113Ser missense_variant 1.0 pyrazinamide
embR 1417613 c.-266C>G upstream_gene_variant 1.0 ethambutol
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.39 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.35 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.35 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.39 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.37 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.37 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.39 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Uncertain significance
amikacin Not assoc w R
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.39 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.47 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.74 capreomycin
linezolid
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.78 capreomycin
linezolid
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.82 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.8 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.79 capreomycin
linezolid
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.83 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.83 capreomycin
linezolid
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.84 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.85 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.88 capreomycin
linezolid
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.85 capreomycin
linezolid
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.86 capreomycin
linezolid
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.84 capreomycin
linezolid
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.83 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.4 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476753 n.3099delG non_coding_transcript_exon_variant 1.0 capreomycin
linezolid
inhA 1673233 c.-969T>G upstream_gene_variant 1.0 isoniazid
ethionamide
rpsA 1833593 c.53delC frameshift_variant 1.0 pyrazinamide Uncertain significance
rpsA 1834884 p.Gln448Leu missense_variant 1.0 pyrazinamide
ahpC 2725932 c.-261G>A upstream_gene_variant 1.0 isoniazid
pepQ 2859739 p.Ala227Gly missense_variant 1.0 bedaquiline
clofazimine
pepQ 2860197 c.222T>C synonymous_variant 1.0 bedaquiline
clofazimine
Rv2681 2997172 p.Asp145Gly missense_variant 1.0 capreomycin
fbiA 3640691 p.Asp50Val missense_variant 1.0 pretomanid
delamanid
clofazimine
fbiA 3641204 p.Gly221Asp missense_variant 1.0 pretomanid
delamanid
clofazimine
clpC1 4039961 p.Tyr248* stop_gained 1.0 pyrazinamide
embB 4248081 c.1569dupG frameshift_variant 0.91 ethambutol