TB-Profiler result

Run: SRR5341377
Summary

Run ID: SRR5341377

Sample name:

Date: 2024-10-05T07:48:06.819054

Number of reads: 2504494

Percentage reads mapped: 93.46

Median coverage: 62.0

Strain: lineage1.1.2;lineage3.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage3 East-African-Indian RD750 0.89
lineage1.1.2 Indo-Oceanic RD239 0.13
lineage3.1.2 East-African-Indian RD750 0.9
lineage1.1 Indo-Oceanic RD239 0.09
lineage1 Indo-Oceanic RD239 0.07
lineage3.1.2.1 East-African-Indian RD750 0.89
lineage3.1 East-African-Indian RD750 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
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
gyrB 6112 p.Met291Ile missense_variant 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.24 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
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 8234 c.933T>G synonymous_variant 0.16 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.14 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.1 isoniazid 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
Rv0565c 657081 c.390G>A synonymous_variant 0.9 ethionamide Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.19 rifampicin Not assoc w R
nusG 734118 c.-136C>T upstream_gene_variant 0.18 rifampicin Uncertain significance
rpoB 759746 c.-61C>T upstream_gene_variant 0.92 rifampicin Not assoc w R
rpoB 760490 c.684C>T synonymous_variant 0.16 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.91 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.16 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.15 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.12 rifampicin Not assoc w R
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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1253330 p.Gly402Glu missense_variant 0.92 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
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
sigE 1364490 c.78T>C synonymous_variant 0.85 pyrazinamide
embR 1417019 p.Cys110Tyr missense_variant 0.12 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.11 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.18 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.12 linezolid Not assoc w R
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
PPE35 2168604 p.Pro670Leu missense_variant 0.87 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 2289047 c.195C>T synonymous_variant 0.93 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.85 pyrazinamide
ahpC 2726105 c.-88G>A upstream_gene_variant 0.9 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.89 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.11 pyrazinamide Not assoc w R - Interim
panD 4044740 c.-459C>T upstream_gene_variant 0.2 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.87 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.9 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 4241042 p.Asn394Asp missense_variant 0.16 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.91 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.17 ethambutol Not assoc w R
embB 4246829 p.Gly106Ser missense_variant 0.78 ethambutol
embB 4247337 p.Thr275Asn missense_variant 0.84 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 0.15 ethambutol Not assoc w R
ubiA 4269031 p.Gly268Asp missense_variant 0.23 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.11 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.17 ethambutol Not assoc w R
whiB6 4338242 p.Gln94Glu missense_variant 0.49 kanamycin Uncertain significance
capreomycin Uncertain significance
amikacin 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 4338603 c.-82C>T upstream_gene_variant 0.13 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 4407873 c.330G>T synonymous_variant 0.15 streptomycin Not assoc w R
gid 4408070 p.Trp45Arg missense_variant 0.86 streptomycin Uncertain significance