TB-Profiler result

Run: SRR25340836
Summary

Run ID: SRR25340836

Sample name:

Date: 2024-04-15T23:24:36.444956

Number of reads: 4140292

Percentage reads mapped: 99.27

Median coverage: 125.0

Strain: lineage1.2.2.2;lineage3

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 0.17
lineage1.2.2 Indo-Oceanic RD239 0.8
lineage1.2.2.2 Indo-Oceanic RD239 0.82
lineage1 Indo-Oceanic RD239 0.82
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 5075 c.-165C>T upstream_gene_variant 0.84 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.82 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 0.73 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 0.99 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.76 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.82 isoniazid Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.83 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.83 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 1.0 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575273 c.-75G>T upstream_gene_variant 0.85 ethionamide
isoniazid
Rv0565c 657081 c.390G>A synonymous_variant 0.25 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.78 ethionamide
hadA 731682 c.-248C>T upstream_gene_variant 0.79 isoniazid
nusG 734116 c.-138T>C upstream_gene_variant 0.77 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.16 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.24 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 0.77 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.77 rifampicin Not assoc w R
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
mmpR5 778433 c.-557G>A upstream_gene_variant 0.31 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rpsL 781420 c.-140C>T upstream_gene_variant 0.16 streptomycin
rplC 800357 c.-452C>A upstream_gene_variant 0.78 linezolid 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
embR 1417019 p.Cys110Tyr missense_variant 0.78 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.83 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.81 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
tsnR 1853974 c.369C>T synonymous_variant 0.82 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
bacA 2062922 p.Ile603Val missense_variant 0.78 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2156355 c.-244C>T upstream_gene_variant 0.74 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.82 pyrazinamide Uncertain significance
PPE35 2169938 c.675C>T synonymous_variant 0.82 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 0.83 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223051 c.114G>A synonymous_variant 0.83 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223553 c.-389C>A upstream_gene_variant 0.78 clofazimine Not assoc w R
bedaquiline Uncertain significance
pncA 2289047 c.195C>T synonymous_variant 0.13 pyrazinamide Not assoc w R
kasA 2518132 c.18C>T synonymous_variant 0.8 isoniazid
kasA 2518505 p.Ala131Thr missense_variant 0.17 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.74 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.27 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.25 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 2782923 p.Asp374Asn missense_variant 0.82 ethambutol Uncertain significance
moxifloxacin
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
pepQ 2859606 c.813G>A synonymous_variant 0.77 clofazimine
bedaquiline
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.77 ethionamide Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.78 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3626467 c.147G>A synonymous_variant 0.77 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.78 pyrazinamide Not assoc w R - Interim
panD 4044703 c.-422C>G upstream_gene_variant 0.17 pyrazinamide
panD 4044872 c.-591C>T upstream_gene_variant 0.18 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.88 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.18 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 4240671 p.Thr270Ile missense_variant 0.83 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.88 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.22 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243168 c.-65C>T upstream_gene_variant 0.81 ethambutol
embA 4245969 p.Pro913Ser missense_variant 0.89 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.85 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.84 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.75 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.82 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.89 ethionamide Uncertain significance
ethA 4328322 c.-849G>T upstream_gene_variant 0.28 ethionamide
whiB6 4338203 p.Arg107Cys missense_variant 0.89 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
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 4338603 c.-82C>T upstream_gene_variant 0.83 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 4407848 p.Ala119Thr missense_variant 0.88 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.9 streptomycin Not assoc w R
gid 4408044 c.159C>T synonymous_variant 0.19 streptomycin