TB-Profiler result

Run: SRR13861409
Summary

Run ID: SRR13861409

Sample name:

Date: 2025-09-15T16:16:44.589292

Number of reads: 1722430

Percentage reads mapped: 43.1

Median coverage: 57.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: HR-TB

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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 katG c.1700delT Assoc w R High-level resistance
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
katG 2154411 c.1700delT frameshift_variant 1.0 isoniazid Assoc w R High-level resistance
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
gyrA 7949 c.648G>T synonymous_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8123 p.Leu274Phe missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9768 p.Gly823Cys missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
Rv0565c 657349 p.Glu41Val missense_variant 1.0 ethionamide Uncertain significance
mmaA3 738066 c.84C>T synonymous_variant 1.0 isoniazid Uncertain significance
rpoC 763734 p.Pro122Leu missense_variant 1.0 rifampicin Uncertain significance
Rv1129c 1253309 p.His409Pro missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
rrs 1472936 n.1091C>T non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.13 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.14 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 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.14 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 0.14 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.15 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.39 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 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.36 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.37 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.39 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.4 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.38 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.35 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.34 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.33 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476640 n.2983C>A non_coding_transcript_exon_variant 1.0 capreomycin Uncertain significance
linezolid Uncertain significance
tsnR 1853566 c.-40C>T upstream_gene_variant 1.0 linezolid Uncertain significance
tlyA 1918034 p.Val32Ala missense_variant 1.0 capreomycin Uncertain significance
bacA 2064615 p.Leu38Phe missense_variant 0.98 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
katG 2155918 p.Ala65Val missense_variant 1.0 isoniazid Uncertain significance
PPE35 2168767 p.Ser616Gly missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170815 c.-203C>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222377 p.Val263Gly missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv2477c 2783104 c.939C>A synonymous_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
ribD 2986993 p.Gly52Val missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2752c 3065787 c.405G>C synonymous_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv3083 3448649 p.Arg49Pro missense_variant 1.0 ethionamide Uncertain significance
Rv3236c 3613067 p.Val17Gly missense_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3613315 c.-199T>G upstream_gene_variant 1.0 pyrazinamide Uncertain significance
fbiA 3640435 c.-108A>C upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3878982 c.-475A>T upstream_gene_variant 1.0 rifampicin Uncertain significance
clpC1 4039842 c.862_863insT frameshift_variant 1.0 pyrazinamide Uncertain significance
panD 4044103 p.Ile60Ser missense_variant 1.0 pyrazinamide Uncertain significance
embA 4245031 p.Arg600Gln missense_variant 1.0 ethambutol Uncertain significance
gid 4408218 c.-16G>T upstream_gene_variant 1.0 streptomycin Uncertain significance