TB-Profiler result

Run: SRR13861596
Summary

Run ID: SRR13861596

Sample name:

Date: 2025-09-15T16:25:01.081200

Number of reads: 1428964

Percentage reads mapped: 28.61

Median coverage: 47.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Other

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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 rrs n.277G>C Mutation from literature
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
rrs 1472122 n.277G>C non_coding_transcript_exon_variant 0.86 streptomycin Mutation from literature
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 5319 p.Arg27Leu missense_variant 0.97 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
mshA 575032 c.-316A>G upstream_gene_variant 0.98 ethionamide Uncertain significance
isoniazid Uncertain significance
rpoB 760867 p.Gly354Asp missense_variant 0.95 rifampicin Uncertain significance
rpoB 762496 c.2691delC frameshift_variant 0.86 rifampicin Uncertain significance
rpoC 764434 c.1065A>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 764446 c.1077T>C synonymous_variant 0.2 rifampicin Uncertain significance
rpoC 764793 p.Met475Arg missense_variant 0.94 rifampicin Uncertain significance
rpoC 766483 c.3114G>C synonymous_variant 0.18 rifampicin Uncertain significance
rpoC 766484 p.Val1039Ile missense_variant 0.17 rifampicin Uncertain significance
rpoC 766492 c.3123T>C synonymous_variant 0.18 rifampicin Uncertain significance
rpoC 766495 c.3126C>T synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766563 p.Thr1065Ser missense_variant 0.85 rifampicin Uncertain significance
rpoC 766933 c.3564A>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoC 766945 c.3576A>G synonymous_variant 0.19 rifampicin Not assoc w R - Interim
rpoC 766963 c.3594T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766978 c.3609C>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoC 766996 c.3627C>T synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767009 c.3640_3642delTCGinsAGC synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 767014 c.3645G>C synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 767033 c.3664_3666delTCGinsAGT synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 767059 c.3690T>G synonymous_variant 0.17 rifampicin Not assoc w R - Interim
rpoC 767062 c.3693C>A synonymous_variant 0.19 rifampicin Uncertain significance
rpoC 767074 c.3705T>C synonymous_variant 0.17 rifampicin Uncertain significance
rpoC 767098 c.3729T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
mmpL5 775976 c.2505G>C synonymous_variant 0.95 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776814 p.Gln556Arg missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rplC 800623 c.-186A>C upstream_gene_variant 0.91 linezolid Uncertain significance
rplC 800769 c.-40A>T upstream_gene_variant 0.91 linezolid Uncertain significance
Rv1129c 1253289 c.1246C>T synonymous_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
fbiC 1302878 c.-53C>G upstream_gene_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fbiC 1303535 p.Ser202Leu missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1407569 c.-229C>A upstream_gene_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
atpE 1461256 p.Met71Arg missense_variant 0.96 bedaquiline Uncertain significance
rrs 1471638 n.-208T>C upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1471836 n.-10A>G upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1473937 n.280C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475333 n.1676T>C non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475355 n.1698C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475369 n.1712G>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1475419 n.1762C>T non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid 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 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.55 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 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.52 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 0.52 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.49 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.5 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.5 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 0.17 capreomycin Not assoc w R
linezolid Uncertain significance
bacA 2063043 c.1686T>A synonymous_variant 0.98 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
katG 2156157 c.-46C>A upstream_gene_variant 1.0 isoniazid Uncertain significance
PPE35 2168627 p.Ile662Met missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2222100 c.1065T>A synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
pncA 2289242 c.-1T>C upstream_gene_variant 1.0 pyrazinamide Uncertain significance
Rv2477c 2783664 c.378delA frameshift_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783794 c.249G>A synonymous_variant 0.16 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783815 c.228A>G synonymous_variant 0.16 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783833 c.210G>C synonymous_variant 0.19 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783843 p.Gly67Asp missense_variant 0.19 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783860 p.Asp61Glu missense_variant 0.21 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783863 c.180C>T synonymous_variant 0.17 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783883 c.160T>C synonymous_variant 0.17 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783884 c.159T>C synonymous_variant 0.17 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
Rv2477c 2783887 c.156C>G synonymous_variant 0.19 amikacin Not assoc w R - Interim
ethambutol Not assoc w R - Interim
kanamycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
Rv2477c 2783920 c.123G>C synonymous_variant 0.2 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
ribD 2987205 p.Ser123Ala missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
ribD 2987347 p.Pro170Leu missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2680 2995859 c.-246C>A upstream_gene_variant 1.0 capreomycin Uncertain significance
Rv2681 2997492 p.Val252Phe missense_variant 1.0 capreomycin Uncertain significance
Rv3083 3448903 p.Asp134His missense_variant 1.0 ethionamide Uncertain significance
lpqB 3624372 p.Val180Ala missense_variant 0.95 bedaquiline Uncertain significance
rifampicin Uncertain significance
mtrA 3627051 p.Asp100Val missense_variant 0.95 bedaquiline Uncertain significance
rifampicin Uncertain significance
rpoA 3877656 c.852T>C synonymous_variant 0.16 rifampicin Not assoc w R - Interim
rpoA 3877743 c.765T>C synonymous_variant 0.13 rifampicin Not assoc w R - Interim
rpoA 3877770 c.738A>G synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3877776 c.732T>C synonymous_variant 0.14 rifampicin Not assoc w R - Interim
rpoA 3878376 c.132G>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoA 3878385 c.123C>G synonymous_variant 0.14 rifampicin Uncertain significance
rpoA 3878391 c.117T>C synonymous_variant 0.14 rifampicin Uncertain significance
rpoA 3878396 c.112C>T synonymous_variant 0.14 rifampicin Uncertain significance
clpC1 4039663 p.Gly348Ser missense_variant 0.96 pyrazinamide Uncertain significance
embC 4241256 p.Arg465Thr missense_variant 1.0 ethambutol Uncertain significance
embA 4246449 p.Val1073Phe missense_variant 1.0 ethambutol Uncertain significance
embB 4248097 c.1584C>G synonymous_variant 0.16 ethambutol Uncertain significance
embB 4248127 c.1614G>C synonymous_variant 0.13 ethambutol Uncertain significance
embB 4248133 c.1620C>G synonymous_variant 0.18 ethambutol Uncertain significance
embB 4248157 c.1644A>G synonymous_variant 0.19 ethambutol Not assoc w R - Interim
aftB 4268192 c.645G>C synonymous_variant 1.0 ethambutol Uncertain significance