TB-Profiler result

Run: SRR13861564
Summary

Run ID: SRR13861564

Sample name:

Date: 2025-09-15T17:53:25.440313

Number of reads: 1416130

Percentage reads mapped: 35.44

Median coverage: 47.0

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
dnaA 1204 c.1204C>T synonymous_variant 0.13 isoniazid Uncertain significance
gyrB 6715 c.1476C>T synonymous_variant 0.98 levofloxacin Uncertain significance
moxifloxacin Not assoc w R - Interim
gyrA 8636 c.1335A>G synonymous_variant 0.13 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
fgd1 491217 c.435T>C synonymous_variant 0.15 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 491232 c.450T>C synonymous_variant 0.14 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 491241 p.Asp153Glu missense_variant 0.15 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 491244 c.462T>C synonymous_variant 0.17 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
mshA 575693 p.Pro116Ala missense_variant 0.96 ethionamide Uncertain significance
isoniazid Uncertain significance
nusG 734493 p.Phe80Leu missense_variant 0.91 rifampicin Uncertain significance
rpoB 759863 p.Gln19His missense_variant 1.0 rifampicin Uncertain significance
rpoB 760399 p.Val198Ala missense_variant 0.93 rifampicin Uncertain significance
rpoB 763150 p.Phe1115Tyr missense_variant 0.9 rifampicin Uncertain significance
rpoC 764516 p.Asp383Asn missense_variant 0.9 rifampicin Uncertain significance
rpoC 766103 p.Arg912Gly missense_variant 0.95 rifampicin Uncertain significance
mmpL5 777066 p.Ile472Ser missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
rpsL 781333 c.-227C>G upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 800612 c.-197A>G upstream_gene_variant 0.14 linezolid Uncertain significance
rplC 800618 c.-191T>C upstream_gene_variant 0.16 linezolid Uncertain significance
rplC 800648 c.-161A>C upstream_gene_variant 0.14 linezolid Uncertain significance
embR 1417750 c.-403G>C upstream_gene_variant 1.0 ethambutol Uncertain significance
rrl 1476336 n.2679C>T non_coding_transcript_exon_variant 0.42 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 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476381 n.2724G>C non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476382 n.2725A>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476383 n.2726T>G non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476384 n.2727G>T non_coding_transcript_exon_variant 0.54 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476408 n.2751G>A non_coding_transcript_exon_variant 0.55 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476411 n.2754G>A non_coding_transcript_exon_variant 0.54 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 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476442 n.2785T>A non_coding_transcript_exon_variant 0.57 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476443 n.2786G>T non_coding_transcript_exon_variant 0.56 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476455 n.2798C>A non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476456 n.2799A>T non_coding_transcript_exon_variant 0.53 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476463 n.2806C>T non_coding_transcript_exon_variant 0.51 capreomycin Uncertain significance
linezolid Uncertain significance
rrl 1476466 n.2809C>T non_coding_transcript_exon_variant 0.49 capreomycin Not assoc w R
linezolid Uncertain significance
inhA 1674507 c.306G>C synonymous_variant 0.13 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674537 c.336C>G synonymous_variant 0.14 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674542 p.Ala114Glu missense_variant 0.14 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674549 c.348G>C synonymous_variant 0.14 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674555 c.354G>A synonymous_variant 0.14 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R - Interim
inhA 1674564 c.363C>T synonymous_variant 0.14 ethionamide Uncertain significance
isoniazid Not assoc w R - Interim
inhA 1674582 c.381T>C synonymous_variant 0.14 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674585 c.384T>C synonymous_variant 0.17 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674589 p.Met130Leu missense_variant 0.18 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674624 c.423A>C synonymous_variant 0.18 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674627 c.426T>G synonymous_variant 0.2 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674630 c.429C>G synonymous_variant 0.2 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674636 c.435C>G synonymous_variant 0.2 ethionamide Uncertain significance
isoniazid Uncertain significance
bacA 2063818 c.910delC frameshift_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
ndh 2103185 c.-143A>C upstream_gene_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
PPE35 2168894 c.1718dupG frameshift_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170039 p.Ala192Thr missense_variant 1.0 pyrazinamide Uncertain significance
Rv1979c 2221777 p.Ala463Val missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
kasA 2518793 p.Ser227Thr missense_variant 0.94 isoniazid Uncertain significance
ahpC 2726300 c.108C>A synonymous_variant 0.96 isoniazid Uncertain significance
folC 2747094 p.Asp169His missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2752c 3064936 p.Ser419* stop_gained 0.98 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3065523 c.669C>T synonymous_variant 0.98 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066039 c.153C>T synonymous_variant 0.91 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
lpqB 3623677 p.Val412Phe missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
alr 3841286 c.63T>A synonymous_variant 1.0 cycloserine Uncertain significance
clpC1 4039268 c.1437C>G synonymous_variant 0.12 pyrazinamide Uncertain significance
clpC1 4039274 c.1431G>C synonymous_variant 0.14 pyrazinamide Not assoc w R - Interim
clpC1 4039286 c.1419T>C synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039289 c.1416T>C synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039295 c.1410A>C synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039298 c.1407T>C synonymous_variant 0.13 pyrazinamide Uncertain significance
clpC1 4039368 p.Lys446Thr missense_variant 0.91 pyrazinamide Uncertain significance
clpC1 4039553 c.1152C>G synonymous_variant 0.12 pyrazinamide Uncertain significance
embC 4241777 p.Gly639Ser missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269888 c.-55C>A upstream_gene_variant 1.0 ethambutol Uncertain significance