TB-Profiler result

Run: SRR13861444
Summary

Run ID: SRR13861444

Sample name:

Date: 2025-09-15T16:16:56.964853

Number of reads: 1071383

Percentage reads mapped: 17.87

Median coverage: 34.0

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 6561 p.Lys441Arg missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7705 p.Thr135Ser missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8409 p.Leu370Ile missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0010c 13327 p.Leu78Ile missense_variant 1.0 isoniazid Uncertain significance
ccsA 619637 c.-254T>G upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
ccsA 620157 c.267G>T synonymous_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
rplC 801215 c.408delC frameshift_variant 1.0 linezolid Uncertain significance
Rv1129c 1253639 p.Leu299* stop_gained 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
fbiC 1304409 c.1479C>G synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1304501 p.Ala524Gly missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
sigE 1365081 c.669G>T synonymous_variant 1.0 pyrazinamide Uncertain significance
rrs 1472791 n.946G>C non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.23 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.22 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.26 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.24 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.24 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.24 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.25 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.23 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.25 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.26 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.27 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.26 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.26 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 0.25 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.24 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.23 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.23 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.26 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.69 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.73 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.75 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.78 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.77 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.76 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.74 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.74 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C 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 Uncertain significance
kasA 2519179 c.1065G>C synonymous_variant 1.0 isoniazid Uncertain significance
folC 2746546 p.Asp351Glu missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2477c 2784407 c.-365A>G upstream_gene_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2680 2996063 c.-42G>C upstream_gene_variant 1.0 capreomycin Uncertain significance
thyX 3068038 c.-93C>A upstream_gene_variant 0.96 para-aminosalicylic_acid Uncertain significance
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 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612721 c.396G>T synonymous_variant 1.0 pyrazinamide Uncertain significance
fbiA 3641221 p.Pro227Ala missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3879230 c.-723C>G upstream_gene_variant 1.0 rifampicin Uncertain significance
clpC1 4039647 p.Glu353Ala missense_variant 1.0 pyrazinamide Uncertain significance
clpC1 4040955 c.-251A>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
embC 4239484 c.-379T>C upstream_gene_variant 1.0 ethambutol Uncertain significance
embC 4240006 c.144A>C synonymous_variant 1.0 ethambutol Uncertain significance
embA 4244074 p.Ala281Val missense_variant 1.0 ethambutol Uncertain significance
embA 4245739 p.Arg836His missense_variant 1.0 ethambutol Uncertain significance
ethA 4326731 p.Ala248Gly missense_variant 1.0 ethionamide Uncertain significance
ethR 4327623 c.75_76insC frameshift_variant 1.0 ethionamide Uncertain significance
gid 4408334 c.-132G>T upstream_gene_variant 0.97 streptomycin Uncertain significance