TB-Profiler result

Run: SRR25827350
Summary

Run ID: SRR25827350

Sample name:

Date: 2024-04-16T09:14:07.005342

Number of reads: 6890073

Percentage reads mapped: 99.02

Median coverage: 237.0

Strain: lineage2.2.1;lineage3

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.28
lineage2 East-Asian RD105 0.68
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.7
lineage2.2 East-Asian (Beijing) RD105;RD207 0.71
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
rpoC p.Ile491Thr Uncertain significance Mutation from literature
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-16C>T Uncertain significance Mutation from literature
embB p.Asp1024Asn Uncertain significance Mutation from literature
pyrazinamide pncA p.Ile5Ser Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Ala90Val Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Asp94Asn Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Asp94Asn Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-12C>T Assoc w R
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid thyA p.Thr22Ala Mutation from literature
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
gyrA 7570 p.Ala90Val missense_variant 0.32 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7581 p.Asp94Asn missense_variant 0.66 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpoC 764841 p.Ile491Thr missense_variant 0.69 rifampicin Uncertain significance Mutation from literature
rpsL 781687 p.Lys43Arg missense_variant 0.7 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2289228 p.Ile5Ser missense_variant 0.63 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 0.76 kanamycin Assoc w R
thyA 3074408 p.Thr22Ala missense_variant 0.71 para-aminosalicylic_acid Mutation from literature
embA 4243217 c.-16C>T upstream_gene_variant 0.55 ethambutol Uncertain significance Mutation from literature
embB 4249583 p.Asp1024Asn missense_variant 0.42 ethambutol Uncertain significance Mutation from literature
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 490717 c.-66C>T upstream_gene_variant 0.24 clofazimine
pretomanid
delamanid
fgd1 491290 p.Val170Met missense_variant 0.75 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575907 p.Ala187Val missense_variant 0.67 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.73 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.64 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.26 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.36 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764916 p.Leu516Pro missense_variant 0.31 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 0.99 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.67 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.7 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254056 p.Asp160Ala missense_variant 0.13 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.72 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834002 p.Glu154Ala missense_variant 0.25 pyrazinamide
rpsA 1834177 c.636A>C synonymous_variant 0.69 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 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
pncA 2289047 c.195C>T synonymous_variant 0.37 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.28 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.3 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.27 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
kanamycin Not assoc w R
rifampicin Not assoc w R
amikacin Not assoc w R
thyX 3067949 c.-4C>T upstream_gene_variant 0.74 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3236c 3612813 p.Thr102Ala missense_variant 0.67 pyrazinamide 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 0.73 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044703 c.-422C>G upstream_gene_variant 0.23 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.25 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.4 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.51 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.45 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.55 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.17 ethambutol
embB 4247847 p.Gln445Arg missense_variant 0.61 ethambutol Uncertain significance
aftB 4267647 p.Asp397Gly missense_variant 0.73 ethambutol Not assoc w R
whiB6 4338292 p.Ala77Val missense_variant 0.75 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 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.7 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.73 streptomycin Not assoc w R