TB-Profiler result

Run: SRR13861551
Summary

Run ID: SRR13861551

Sample name:

Date: 2025-09-15T16:17:53.285126

Number of reads: 3117212

Percentage reads mapped: 78.01

Median coverage: 105.0

Strain: lineage4.9

Spoligotype:

Drug-resistance: Sensitive

Download CSV Download TXT Download JSON
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
ccsA 620144 c.255dupT frameshift_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
hadA 731898 c.-32T>A upstream_gene_variant 1.0 isoniazid Uncertain significance
rpoB 760191 p.Val129Phe missense_variant 1.0 rifampicin Uncertain significance
rpoB 760311 p.Val169Leu missense_variant 1.0 rifampicin Uncertain significance
rpoB 762805 p.Gly1000Asp missense_variant 1.0 rifampicin Uncertain significance
rpoB 762963 p.Gly1053Arg missense_variant 1.0 rifampicin Uncertain significance
rpoC 763662 p.Ala98Asp missense_variant 1.0 rifampicin Uncertain significance
mmpL5 776041 p.Ala814Thr missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 776070 c.2410delA frameshift_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpL5 777800 c.681C>T synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1129c 1253473 p.Phe354Leu missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1254207 p.Val110Phe missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
fbiC 1304996 p.Leu689Ser missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
Rv1258c 1407148 p.Ala65Ser missense_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
Rv1258c 1407602 c.-262G>T upstream_gene_variant 1.0 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
embR 1416842 p.Asp169Gly missense_variant 1.0 ethambutol Uncertain significance
embR 1417911 c.-564A>T upstream_gene_variant 1.0 ethambutol Uncertain significance
rrl 1476357 n.2700T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476358 n.2701T>C non_coding_transcript_exon_variant 0.11 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476359 n.2702C>G non_coding_transcript_exon_variant 0.12 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476369 n.2712C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476425 n.2768G>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476429 n.2772A>C non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.15 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.16 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.14 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.14 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674940 c.739_740insG frameshift_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
ndh 2102694 p.Val117Ile missense_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2155865 p.Val83Met missense_variant 1.0 isoniazid Uncertain significance
katG 2156606 c.-495T>C upstream_gene_variant 1.0 isoniazid Uncertain significance
PPE35 2168123 c.2489dupG frameshift_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170268 c.345C>A synonymous_variant 1.0 pyrazinamide Uncertain significance
kasA 2518311 p.Asp66Gly missense_variant 1.0 isoniazid Uncertain significance
eis 2714666 p.Tyr223Asp missense_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2726589 p.Arg133Ser missense_variant 1.0 isoniazid Uncertain significance
Rv2752c 3066289 c.-98T>G upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
thyA 3074418 p.Lys18Asn missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
ald 3087163 c.344_345insC frameshift_variant 1.0 cycloserine Uncertain significance
Rv3236c 3612049 c.1068G>C synonymous_variant 1.0 pyrazinamide Uncertain significance
Rv3236c 3612400 c.717G>A synonymous_variant 1.0 pyrazinamide Uncertain significance
fbiB 3642445 p.Ala304Gly missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
rpoA 3879139 c.-633dupA upstream_gene_variant 1.0 rifampicin Uncertain significance
clpC1 4038941 c.1764G>C synonymous_variant 1.0 pyrazinamide Uncertain significance
clpC1 4040104 p.Met201Leu missense_variant 0.99 pyrazinamide Uncertain significance
embC 4241480 c.1618T>C synonymous_variant 1.0 ethambutol Uncertain significance
embB 4249483 c.2970C>G synonymous_variant 1.0 ethambutol Uncertain significance
aftB 4268164 c.672_673insA frameshift_variant 0.98 ethambutol Uncertain significance
ethA 4327641 c.-168G>A upstream_gene_variant 1.0 ethionamide Uncertain significance