TB-Profiler result

Run: SRR24083713
Summary

Run ID: SRR24083713

Sample name:

Date: 2024-04-16T06:43:31.391219

Number of reads: 5007782

Percentage reads mapped: 99.57

Median coverage: 124.0

Strain: lineage2.1;lineage4.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 0.34
lineage4.1 Euro-American None 0.67
lineage4.1.2 Euro-American None 0.69
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.64
lineage4 Euro-American None 0.68
lineage2.1 East-Asian (non-Beijing) None 0.26
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
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 0.68 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.29 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.73 ethionamide Not assoc w R
isoniazid Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.37 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.34 ethionamide Uncertain significance
Rv0565c 657269 p.Ser68Pro missense_variant 0.6 ethionamide Uncertain significance
rpoB 760115 c.309C>T synonymous_variant 0.71 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.39 rifampicin Not assoc w R
rpoC 765121 c.1752G>A synonymous_variant 0.15 rifampicin Not assoc w R - Interim
rpoC 765150 p.Gly594Glu missense_variant 0.77 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.36 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpS5 778706 p.Val67Gly missense_variant 0.35 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781276 c.-284A>C upstream_gene_variant 0.72 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.44 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1303596 c.666G>A synonymous_variant 0.38 clofazimine
pretomanid
delamanid
fbiC 1304443 p.Ala505Thr missense_variant 0.31 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.29 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
katG 2154724 p.Arg463Leu missense_variant 0.36 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.36 pyrazinamide Not assoc w R
PPE35 2170235 c.378T>C synonymous_variant 0.3 pyrazinamide
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2288797 p.Asn149Asp missense_variant 0.62 pyrazinamide Uncertain significance
kasA 2518076 c.-39C>T upstream_gene_variant 0.65 isoniazid
Rv2477c 2783790 p.Val85Ile missense_variant 0.2 ethambutol Not assoc w R
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568431 c.249C>G synonymous_variant 0.14 streptomycin
amikacin
kanamycin
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040841 c.-138delG upstream_gene_variant 0.25 pyrazinamide
glpK 4138381 p.Gly459Ser missense_variant 0.72 ethambutol
moxifloxacin
streptomycin
levofloxacin
rifampicin
isoniazid
glpK 4139183 c.572dupG frameshift_variant 0.18 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
embC 4239298 c.-565C>T upstream_gene_variant 0.74 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 0.63 ethambutol Not assoc w R
embA 4246088 c.2856A>G synonymous_variant 0.3 ethambutol Not assoc w R
embB 4249151 p.Ala880Thr missense_variant 0.19 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.32 ethambutol Not assoc w R
ethA 4328307 c.-834C>T upstream_gene_variant 0.29 ethionamide
whiB6 4338475 p.Trp16Ser missense_variant 0.25 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.32 streptomycin Not assoc w R