TB-Profiler result

Run: SRR13861492
Summary

Run ID: SRR13861492

Sample name:

Date: 2025-09-15T16:24:24.151258

Number of reads: 1757069

Percentage reads mapped: 35.18

Median coverage: 59.0

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 100.0
lineage4.9 Euro-American (H37Rv-like) None 100.0
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 5624 p.Asn129Asp missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 575194 c.-154G>T upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
hadA 731960 p.His11Asp missense_variant 1.0 isoniazid Uncertain significance
hadA 732111 p.Cys61Tyr missense_variant 1.0 isoniazid Uncertain significance
mmaA3 737975 p.Leu59Val missense_variant 1.0 isoniazid Uncertain significance
rpoB 760907 c.1101_1102insT frameshift_variant 1.0 rifampicin Uncertain significance
rplC 801226 p.Gly140Arg missense_variant 1.0 linezolid Uncertain significance
Rv1129c 1253913 p.Ile208Phe missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254602 c.-68C>T upstream_gene_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254678 c.-144A>G upstream_gene_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
sigE 1364750 p.Thr113Ser missense_variant 1.0 pyrazinamide Uncertain significance
embR 1417503 c.-156A>C upstream_gene_variant 1.0 ethambutol Uncertain significance
embR 1417613 c.-266C>G upstream_gene_variant 1.0 ethambutol Uncertain significance
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.16 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.16 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
streptomycin Uncertain significance
rrs 1473002 n.1157G>T non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.17 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.48 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.46 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.5 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.2 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476753 n.3099delG non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673233 c.-969T>G upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1833593 c.53delC frameshift_variant 1.0 pyrazinamide Uncertain significance
rpsA 1834884 p.Gln448Leu missense_variant 1.0 pyrazinamide Uncertain significance
bacA 2064646 p.Thr28Arg missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
PPE35 2169282 p.Arg444His missense_variant 1.0 pyrazinamide Uncertain significance
ahpC 2725932 c.-261G>A upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv2477c 2783645 p.Asp133Gly missense_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
pepQ 2859739 p.Ala227Gly missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
pepQ 2860197 c.222T>C synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2681 2997172 p.Asp145Gly missense_variant 1.0 capreomycin Uncertain significance
Rv3083 3448909 p.Leu136Ile missense_variant 0.98 ethionamide Uncertain significance
mtrA 3627160 p.Gly64Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
fbiA 3640691 p.Asp50Val missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiA 3641204 p.Gly221Asp missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3878967 c.-460G>T upstream_gene_variant 1.0 rifampicin Uncertain significance
clpC1 4039961 p.Tyr248* stop_gained 1.0 pyrazinamide Uncertain significance
glpK 4138333 p.Ser475Pro missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4240818 p.Thr319Arg missense_variant 1.0 ethambutol Uncertain significance
embB 4248081 c.1569dupG frameshift_variant 1.0 ethambutol Uncertain significance
ethA 4327644 c.-171G>A upstream_gene_variant 1.0 ethionamide Uncertain significance