TB-Profiler result

Run: SRR5073667
Summary

Run ID: SRR5073667

Sample name:

Date: 2025-06-01T06:54:38.685392

Number of reads: 2549094

Percentage reads mapped: 99.53

Median coverage: 82.0

Strain: lineage2.2.1;lineage4.1.2.1

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.11
lineage4.1 Euro-American None 0.9
lineage4.1.2 Euro-American None 0.89
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.89
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.1
lineage2.2 East-Asian (Beijing) RD105;RD207 0.08
lineage4 Euro-American None 0.92
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 gid c.102delG Assoc w R
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
gid 4408100 c.102delG frameshift_variant 0.87 streptomycin Assoc w R
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
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.87 clofazimine Not assoc w R
delamanid Uncertain significance
pretomanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.16 clofazimine Not assoc w R
delamanid Not assoc w R - Interim
pretomanid Uncertain significance
mshA 575679 p.Asn111Ser missense_variant 0.9 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657269 p.Ser68Pro missense_variant 0.89 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.89 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.14 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.89 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.14 isoniazid Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.14 isoniazid Uncertain significance
pyrazinamide Uncertain significance
streptomycin Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
streptomycin Uncertain significance
rpsA 1834177 c.636A>C synonymous_variant 0.12 pyrazinamide Not assoc w R - Interim
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
kasA 2518076 c.-39C>T upstream_gene_variant 0.87 isoniazid Uncertain significance
Rv2477c 2783095 c.948C>G synonymous_variant 0.13 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
streptomycin Not assoc w R - Interim
Rv2680 2996034 c.-71G>A upstream_gene_variant 0.14 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.17 capreomycin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine Uncertain significance
fbiD 3339337 p.Gly74Arg missense_variant 0.97 clofazimine Uncertain significance
delamanid Uncertain significance
pretomanid Uncertain significance
lpqB 3624407 c.504C>T synonymous_variant 0.9 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.11 bedaquiline Uncertain significance
rifampicin Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.91 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.87 ethambutol Not assoc w R
embA 4246085 p.Glu951Asp missense_variant 0.16 ethambutol Not assoc w R
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 amikacin Not assoc w R
capreomycin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 amikacin Uncertain significance
capreomycin Uncertain significance
kanamycin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.11 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.12 streptomycin Not assoc w R