TB-Profiler result

Run: SRR13837725
Summary

Run ID: SRR13837725

Sample name:

Date: 2025-03-06T16:42:36.279835

Number of reads: 2936562

Percentage reads mapped: 100.0

Median coverage: 99.0

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
dnaA 442 p.Pro148Ala missense_variant 1.0 isoniazid Uncertain significance
gyrB 6667 p.Gln476His missense_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 7289 c.-13_-12insT upstream_gene_variant 1.0 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rpoB 760214 p.Asn136Lys missense_variant 1.0 rifampicin Uncertain significance
Rv1129c 1253228 p.Asp436Ala missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv1129c 1253885 p.Lys217Arg missense_variant 1.0 isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
fbiC 1304005 p.Pro359Ser missense_variant 1.0 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
sigE 1364782 p.Val124Leu missense_variant 1.0 pyrazinamide Uncertain significance
embR 1417793 c.-446C>T upstream_gene_variant 1.0 ethambutol Uncertain significance
rrs 1471943 n.98T>C non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1472075 n.230A>C non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473066 n.1221A>T non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rrs 1473370 n.1525T>C non_coding_transcript_exon_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
inhA 1673813 c.-389G>T upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674784 p.Arg195Gly missense_variant 0.99 ethionamide Uncertain significance
isoniazid Uncertain significance
bacA 2064693 p.Trp12Cys missense_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
ndh 2101793 p.Trp417* stop_gained 1.0 delamanid Uncertain significance
ethionamide Uncertain significance
isoniazid Uncertain significance
PPE35 2169624 p.Gly330Asp missense_variant 1.0 pyrazinamide Uncertain significance
kasA 2519223 p.Thr370Ile missense_variant 1.0 isoniazid Uncertain significance
ahpC 2726213 c.21C>T synonymous_variant 1.0 isoniazid Uncertain significance
Rv2477c 2783213 p.Ala277Val missense_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 2783662 p.Glu127Asp missense_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 2784275 c.-234dupC upstream_gene_variant 1.0 amikacin Uncertain significance
ethambutol Uncertain significance
kanamycin Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
streptomycin Uncertain significance
ribD 2987016 p.Gly60Arg missense_variant 1.0 para-aminosalicylic_acid Uncertain significance
Rv2680 2996618 p.Trp172Arg missense_variant 1.0 capreomycin Uncertain significance
Rv2681 2997515 c.777T>G synonymous_variant 1.0 capreomycin Uncertain significance
Rv2681 2997779 c.1041C>G synonymous_variant 0.99 capreomycin Uncertain significance
Rv2752c 3065644 p.Thr183Ser missense_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
Rv2752c 3066590 c.-399A>G upstream_gene_variant 1.0 ethambutol Uncertain significance
isoniazid Uncertain significance
levofloxacin Uncertain significance
moxifloxacin Uncertain significance
rifampicin Uncertain significance
thyA 3074595 c.-124C>A upstream_gene_variant 1.0 para-aminosalicylic_acid Uncertain significance
lpqB 3624763 p.Val50Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
lpqB 3625054 c.-144C>G upstream_gene_variant 1.0 bedaquiline Uncertain significance
rifampicin Uncertain significance
alr 3841581 c.-161T>A upstream_gene_variant 1.0 cycloserine Uncertain significance
embC 4242810 p.Leu983Gln missense_variant 1.0 ethambutol Uncertain significance
embB 4246553 p.Arg14Trp missense_variant 1.0 ethambutol Uncertain significance
embB 4248920 p.Val803Met missense_variant 1.0 ethambutol Uncertain significance
embB 4249551 p.Arg1013Leu missense_variant 0.99 ethambutol Uncertain significance
ethA 4326296 p.Leu393Gln missense_variant 1.0 ethionamide Uncertain significance
gid 4408480 c.-278G>C upstream_gene_variant 1.0 streptomycin Uncertain significance