TB-Profiler result

Run: SRR19428517
Summary

Run ID: SRR19428517

Sample name:

Date: 2024-10-05T11:46:47.780138

Number of reads: 1414312

Percentage reads mapped: 99.59

Median coverage: 71.0

Strain: lineage1.1.2;lineage3.1.1;lineage4.3.4.2.1

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 0.75
lineage1.1.2 Indo-Oceanic RD239 0.05
lineage3.1.1 East-African-Indian RD750 0.61
lineage1.1 Indo-Oceanic RD239 0.12
lineage4 Euro-American None 0.12
lineage4.3.4.2.1 Euro-American (LAM) RD174 0.05
lineage1 Indo-Oceanic RD239 0.1
lineage4.3.4 Euro-American (LAM) RD174 0.06
lineage4.3.4.2 Euro-American (LAM) RD174 0.06
lineage3.1 East-African-Indian RD750 0.44
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 0.11 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6140 p.Val301Leu missense_variant 0.11 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 8452 p.Ala384Val missense_variant 0.21 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 13460 c.99T>C synonymous_variant 0.14 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.86 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 574900 c.-448G>C upstream_gene_variant 0.24 isoniazid Uncertain significance
ethionamide Uncertain significance
mshA 575907 p.Ala187Val missense_variant 0.11 isoniazid Not assoc w R
ethionamide Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.75 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.1 ethionamide
rpoB 759746 c.-61C>T upstream_gene_variant 0.55 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.82 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.88 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.11 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 0.79 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 1254253 c.282C>T synonymous_variant 0.12 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
rifampicin Not assoc w R - Interim
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.78 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406349 p.Ile331Ser missense_variant 0.19 streptomycin
pyrazinamide
isoniazid
embR 1417019 p.Cys110Tyr missense_variant 0.11 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.16 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rrs 1472857 n.1012A>G non_coding_transcript_exon_variant 0.16 kanamycin Uncertain significance
capreomycin Uncertain significance
streptomycin Uncertain significance
amikacin Uncertain significance
rrl 1475114 n.1457C>T non_coding_transcript_exon_variant 0.13 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1673283 c.-919A>C upstream_gene_variant 0.14 isoniazid
ethionamide
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917777 c.-163A>G upstream_gene_variant 0.12 capreomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 0.86 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.85 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.12 pyrazinamide Uncertain significance
PPE35 2170461 p.Gly51Glu missense_variant 0.47 pyrazinamide Not assoc w R
Rv1979c 2221783 p.Ala461Glu missense_variant 0.16 bedaquiline Uncertain significance
clofazimine
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 0.54 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.75 pyrazinamide
eis 2714908 p.Val142Gly missense_variant 0.16 kanamycin
amikacin
ahpC 2726051 c.-142G>A upstream_gene_variant 0.23 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.72 isoniazid Not assoc w R
ahpC 2726672 c.480G>A synonymous_variant 0.13 isoniazid Not assoc w R - Interim
Rv2477c 2782498 c.1545C>T synonymous_variant 0.74 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 0.95 cycloserine
Rv3236c 3612009 p.Ala370Thr missense_variant 0.12 pyrazinamide Not assoc w R
Rv3236c 3612870 p.Ala83Ser missense_variant 0.11 pyrazinamide
lpqB 3624486 p.Asp142Gly missense_variant 0.21 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.94 rifampicin Not assoc w R
bedaquiline Uncertain significance
panD 4044872 c.-591C>T upstream_gene_variant 0.65 pyrazinamide
glpK 4138622 c.1134C>T synonymous_variant 0.57 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 4240172 p.Val104Met missense_variant 0.15 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.18 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.57 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.72 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4245166 p.Pro645Gln missense_variant 0.11 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.15 ethambutol Not assoc w R
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
whiB6 4338909 c.-388T>G upstream_gene_variant 0.14 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.95 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.26 streptomycin Not assoc w R