TB-Profiler result

Run: SRR13837716
Summary

Run ID: SRR13837716

Sample name:

Date: 2025-03-09T11:18:58.823515

Number of reads: 2936302

Percentage reads mapped: 100.0

Median coverage: 98.0

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 1.0
lineage4.9 Euro-American (H37Rv-like) None 1.0
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
gyrB 6624 p.Ser462* stop_gained 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7285 c.-17T>C upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8798 c.1497C>T synonymous_variant 1.0 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
mmaA3 737872 p.Asp93Ala missense_variant 1.0 isoniazid Uncertain significance
mmaA3 738202 c.-53A>C upstream_gene_variant 1.0 isoniazid Uncertain significance
rpoC 764438 c.1069_1070insA frameshift_variant 1.0 rifampicin Uncertain significance
mmpL5 775795 p.Ala896Ser missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
fbiC 1303593 c.663G>A synonymous_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
embR 1416428 c.919_920insT frameshift_variant 1.0 ethambutol Uncertain significance
rrs 1471798 n.-48G>A upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472913 n.1068G>C non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrl 1476167 n.2510T>A non_coding_transcript_exon_variant 0.99 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674226 p.Arg9Trp missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
rpsA 1833352 c.-190C>A upstream_gene_variant 1.0 pyrazinamide Uncertain significance
rpsA 1833710 p.Tyr57Asp missense_variant 1.0 pyrazinamide Uncertain significance
rpsA 1834711 c.1170C>T synonymous_variant 1.0 pyrazinamide Uncertain significance
ndh 2102326 c.717G>T synonymous_variant 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
Rv1979c 2222739 c.426C>A synonymous_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2222936 p.Ala77Thr missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
eis 2714217 c.1115dupC frameshift_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
eis 2714361 c.972C>A synonymous_variant 1.0 amikacin Uncertain significance
kanamycin Uncertain significance
ahpC 2725906 c.-287C>G upstream_gene_variant 1.0 isoniazid Uncertain significance
Rv2477c 2782975 c.1068C>T synonymous_variant 1.0 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
pepQ 2859813 p.Ile202Met missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
pepQ 2860286 p.Val45Leu missense_variant 1.0 bedaquiline Uncertain significance
clofazimine Uncertain significance
ribD 2987503 p.Gly222Val missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
ald 3087394 p.Ala192Val missense_variant 1.0 cycloserine Uncertain significance
ald 3087464 c.645C>T synonymous_variant 1.0 cycloserine Uncertain significance
ald 3087512 c.693T>A synonymous_variant 1.0 cycloserine Uncertain significance
Rv3083 3448303 c.-201G>C upstream_gene_variant 1.0 ethionamide Uncertain significance
lpqB 3623311 p.Pro534Ser missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
lpqB 3623400 p.Val504Glu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
lpqB 3624438 p.Gln158Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
rpoA 3879111 c.-604G>C upstream_gene_variant 0.99 rifampicin Uncertain significance
embC 4241874 p.Leu671Arg missense_variant 1.0 ethambutol Uncertain significance
embC 4242816 p.Trp985* stop_gained 0.99 ethambutol Uncertain significance
embB 4248365 p.Val618Met missense_variant 1.0 ethambutol Uncertain significance
aftB 4267893 p.Ile315Ser missense_variant 1.0 ethambutol Uncertain significance
aftB 4268516 c.321A>G synonymous_variant 1.0 ethambutol Not assoc w R - Interim
ethR 4326691 c.-858C>A upstream_gene_variant 1.0 ethionamide Uncertain significance