TB-Profiler result

Run: SRR13861474
Summary

Run ID: SRR13861474

Sample name:

Date: 2025-09-15T16:24:21.079395

Number of reads: 1140377

Percentage reads mapped: 22.83

Median coverage: 38.0

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
gyrA 7877 p.His192Gln missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 576146 p.Val267Leu missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
hadA 732095 p.Pro56Thr missense_variant 1.0 isoniazid Uncertain significance
rpoB 759869 c.63C>T synonymous_variant 1.0 rifampicin Uncertain significance
rpoC 763782 p.Ser138* stop_gained 1.0 rifampicin Uncertain significance
rpoC 764568 p.Lys400Thr missense_variant 1.0 rifampicin Uncertain significance
mmpL5 777073 p.Lys470Glu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 777311 c.1170C>T synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 778981 c.-501C>A upstream_gene_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 801436 p.Ser210Arg missense_variant 1.0 linezolid Uncertain significance
fbiC 1303686 c.756C>G synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rrs 1472605 n.760G>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 0.31 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472956 n.1111T>C non_coding_transcript_exon_variant 0.29 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472957 n.1112C>T non_coding_transcript_exon_variant 0.3 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472958 n.1113A>T non_coding_transcript_exon_variant 0.31 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472959 n.1114T>A non_coding_transcript_exon_variant 0.31 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472963 n.1118G>A non_coding_transcript_exon_variant 0.33 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472971 n.1126G>C non_coding_transcript_exon_variant 0.34 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472973 n.1128_1130delAATinsCG non_coding_transcript_exon_variant 0.35 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472982 n.1137G>C non_coding_transcript_exon_variant 0.33 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472987 n.1142G>T non_coding_transcript_exon_variant 0.32 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472988 n.1143T>A non_coding_transcript_exon_variant 0.32 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472989 n.1144G>A non_coding_transcript_exon_variant 0.32 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472990 n.1145A>G non_coding_transcript_exon_variant 0.32 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 0.31 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473004 n.1159T>A non_coding_transcript_exon_variant 0.32 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473008 n.1163C>A non_coding_transcript_exon_variant 0.31 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473009 n.1164T>C non_coding_transcript_exon_variant 0.29 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473044 n.1199C>G non_coding_transcript_exon_variant 0.29 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.47 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476356 n.2699C>A non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.6 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.59 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.58 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.53 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476506 n.2849T>C non_coding_transcript_exon_variant 0.26 capreomycin Not assoc w R
linezolid Uncertain significance
rrl 1476512 n.2855C>T non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674376 p.Pro59Ser missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
tlyA 1917844 c.-96C>A upstream_gene_variant 1.0 capreomycin Uncertain significance
tlyA 1918260 p.His107Gln missense_variant 1.0 capreomycin Uncertain significance
bacA 2064394 p.Thr112Arg missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
katG 2154461 p.Ala551Pro missense_variant 1.0 isoniazid Uncertain significance
Rv1979c 2222535 c.630C>G synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
kasA 2518608 p.Met165Thr missense_variant 1.0 isoniazid Uncertain significance
eis 2714211 c.1122G>A synonymous_variant 1.0 amikacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
ahpC 2726250 p.Gly20Arg missense_variant 1.0 isoniazid Uncertain significance
Rv2752c 3066461 c.-270C>T upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066855 c.-664T>G upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
whiB7 3568939 c.-260T>C upstream_gene_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612518 p.Tyr200Ser missense_variant 1.0 pyrazinamide Uncertain significance
fbiB 3641684 p.Ser50Arg missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
glpK 4139507 p.Lys83Asn missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
embC 4240263 p.Val134Ala missense_variant 1.0 ethambutol Uncertain significance
embC 4240920 p.Leu353Pro missense_variant 1.0 ethambutol Uncertain significance
embC 4241504 p.Val548Met missense_variant 1.0 ethambutol Uncertain significance
embB 4248000 p.Asp496Val missense_variant 1.0 ethambutol Uncertain significance
aftB 4268715 p.Leu41Pro missense_variant 1.0 ethambutol Uncertain significance
ethR 4327704 p.Lys52Asn missense_variant 1.0 ethionamide Uncertain significance