TB-Profiler result

Run: SRR25827720
Summary

Run ID: SRR25827720

Sample name:

Date: 2024-10-04T12:16:28.813390

Number of reads: 5867974

Percentage reads mapped: 98.88

Median coverage: 200.0

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 0.2
lineage2 East-Asian RD105 0.81
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.77
lineage2.2 East-Asian (Beijing) RD105;RD207 0.8
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
isoniazid inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embA c.-11C>A Uncertain significance Mutation from literature
embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
p.Leu27Pro Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Arg 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.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrA p.Ala90Val Assoc w R
p.Ser91Pro Assoc w R
ciprofloxacin
aminoglycosides
amikacin rrs n.1401A>G Assoc w R
capreomycin rrs n.1401A>G Assoc w R
kanamycin rrs n.1401A>G Assoc w R
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
ethA p.Ser57Tyr Assoc w R - Interim
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
gyrA 7570 p.Ala90Val missense_variant 0.43 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 7572 p.Ser91Pro missense_variant 0.43 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)
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.81 streptomycin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 0.17 streptomycin Assoc w R
rrs 1473246 n.1401A>G non_coding_transcript_exon_variant 0.14 amikacin Assoc w R
capreomycin Assoc w R
kanamycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.6 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.41 pyrazinamide Assoc w R
pncA 2289162 p.Leu27Pro missense_variant 0.21 pyrazinamide Assoc w R
embA 4243222 c.-11C>A upstream_gene_variant 0.2 ethambutol Uncertain significance Mutation from literature
embB 4247429 p.Met306Val missense_variant 0.27 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.73 ethambutol Assoc w R
ethA 4327304 p.Ser57Tyr missense_variant 0.16 ethionamide Assoc w R - Interim
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 7581 p.Asp94Thr missense_variant 0.2 levofloxacin
moxifloxacin
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
Rv0010c 13183 p.Val126Met missense_variant 0.22 isoniazid Uncertain significance
Rv0010c 13906 c.-348C>T upstream_gene_variant 0.38 isoniazid
fgd1 491290 p.Val170Met missense_variant 0.56 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.55 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.8 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 1.0 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.81 ethionamide Uncertain significance
mmaA3 737591 p.Gly187Ser missense_variant 0.25 isoniazid
rpoB 759746 c.-61C>T upstream_gene_variant 0.2 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.22 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764533 c.1164C>A synonymous_variant 0.23 rifampicin Not assoc w R - Interim
rpoC 764840 p.Ile491Val missense_variant 0.59 rifampicin Uncertain significance
rpoC 766488 p.Pro1040Arg missense_variant 0.2 rifampicin Uncertain significance
rpoC 767123 p.Val1252Leu missense_variant 0.26 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.57 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.82 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.79 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.76 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 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.18 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.19 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.26 kanamycin Not assoc w R
levofloxacin Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
amikacin Not assoc w R
Rv2752c 3064700 p.Ser498Pro missense_variant 0.35 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
Rv2752c 3065864 p.Ala110Ser missense_variant 0.41 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3568425 c.255T>G synonymous_variant 0.16 kanamycin
amikacin
streptomycin
whiB7 3568555 p.Leu42Pro missense_variant 0.24 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
whiB7 3568854 c.-176delG upstream_gene_variant 0.2 kanamycin Uncertain significance
amikacin Uncertain significance
streptomycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.82 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.76 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044703 c.-422C>G upstream_gene_variant 0.17 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.2 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.18 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R - Interim
rifampicin Not assoc w R
ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.57 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.17 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 0.71 ethambutol Not assoc w R
embB 4247028 p.Leu172Arg missense_variant 0.22 ethambutol
aftB 4267647 p.Asp397Gly missense_variant 0.72 ethambutol Not assoc w R
ethA 4326593 p.Cys294Phe missense_variant 0.34 ethionamide Uncertain significance
ethA 4326676 p.Ser266Arg missense_variant 0.18 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin Not assoc w R
gid 4407620 p.Tyr195His missense_variant 0.59 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.76 streptomycin Not assoc w R