TB-Profiler result

Run: SRR25827665
Summary

Run ID: SRR25827665

Sample name:

Date: 2024-04-15T18:12:56.640541

Number of reads: 11021769

Percentage reads mapped: 98.49

Median coverage: 365.0

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 0.36
lineage2 East-Asian RD105 0.65
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.64
lineage2.2 East-Asian (Beijing) RD105;RD207 0.65
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Trp Assoc w R
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 embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Gly132Ala Assoc w R
p.Leu27Pro Assoc w R
c.-11A>G Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
rrs n.905C>A Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrB p.Glu501Asp Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrB p.Glu501Asp Assoc w R - Interim
gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
gyrB 6742 p.Glu501Asp missense_variant 0.35 levofloxacin Assoc w R - Interim
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
gyrA 7582 p.Asp94Gly missense_variant 0.27 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Trp missense_variant 0.33 rifampicin Assoc w R
rpoB 761155 p.Ser450Leu missense_variant 0.67 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.68 streptomycin Assoc w R
rrs 1472750 n.905C>A non_coding_transcript_exon_variant 0.41 streptomycin Uncertain significance Mutation from literature
inhA 1673425 c.-777C>T upstream_gene_variant 0.24 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288847 p.Gly132Ala missense_variant 0.26 pyrazinamide Assoc w R
pncA 2289162 p.Leu27Pro missense_variant 0.36 pyrazinamide Assoc w R
pncA 2289252 c.-11A>G upstream_gene_variant 0.35 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.73 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.3 ethambutol 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
gyrB 5078 c.-162_-161insG upstream_gene_variant 0.36 levofloxacin
moxifloxacin
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 491290 p.Val170Met missense_variant 0.24 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 0.23 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.63 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 0.6 ethionamide Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.42 rifampicin Not assoc w R
rpoB 762427 p.Ser874Phe missense_variant 0.36 rifampicin
rpoB 762434 c.2628T>G synonymous_variant 0.38 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 764840 p.Ile491Val missense_variant 0.25 rifampicin Uncertain significance
rpoC 765223 c.1854G>T synonymous_variant 0.3 rifampicin Not assoc w R - Interim
rpoC 766488 p.Pro1040Arg missense_variant 0.42 rifampicin Uncertain significance
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 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776182 p.Asp767Asn missense_variant 0.32 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.67 clofazimine
bedaquiline
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 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 0.63 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.65 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 2222873 p.His98Tyr missense_variant 0.42 clofazimine Uncertain significance
bedaquiline Uncertain significance
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 0.4 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.34 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.37 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.35 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
Rv2477c 2783425 c.618C>T synonymous_variant 0.39 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
whiB7 3569220 c.-541C>T upstream_gene_variant 0.4 streptomycin
amikacin
kanamycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.63 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 0.63 bedaquiline Uncertain significance
rifampicin Not assoc w R
panD 4044872 c.-591C>T upstream_gene_variant 0.37 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.39 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
glpK 4139639 c.117G>C synonymous_variant 0.35 ethambutol Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
levofloxacin Not assoc w R - Interim
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
embC 4241022 p.Ala387Val missense_variant 0.23 ethambutol Uncertain significance
embC 4242075 p.Arg738Gln missense_variant 0.4 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243200 c.-32delG upstream_gene_variant 0.38 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.63 ethambutol Not assoc w R
embB 4249778 p.Trp1089Arg missense_variant 0.39 ethambutol Uncertain significance
aftB 4267337 c.1500C>T synonymous_variant 0.33 ethambutol Not assoc w R - Interim
aftB 4267647 p.Asp397Gly missense_variant 0.57 ethambutol Not assoc w R
ethA 4326676 p.Ser266Arg missense_variant 0.38 ethionamide Uncertain significance
ethA 4326927 p.Ser183Arg missense_variant 0.37 ethionamide 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 4338600 c.-79T>G upstream_gene_variant 0.36 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 0.24 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.61 streptomycin Not assoc w R