TB-Profiler result

Run: SRR19428519
Summary

Run ID: SRR19428519

Sample name:

Date: 2024-10-03T20:41:59.869018

Number of reads: 2314295

Percentage reads mapped: 99.3

Median coverage: 95.0

Strain: lineage1.1.2;lineage3.1.1;lineage4.6.1.1

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 0.27
lineage1.1.2 Indo-Oceanic RD239 0.62
lineage4.6 Euro-American None 0.09
lineage3.1.1 East-African-Indian RD750 0.28
lineage1.1 Indo-Oceanic RD239 0.61
lineage4.6.1.1 Euro-American RD724 0.15
lineage1 Indo-Oceanic RD239 0.59
lineage4.6.1 Euro-American (Uganda) RD724 0.12
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 0.6 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.61 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 0.65 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.51 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 13298 p.Ile87Met missense_variant 0.69 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.63 isoniazid Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.89 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575080 c.-268A>G upstream_gene_variant 0.22 isoniazid Uncertain significance
ethionamide Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.27 ethionamide Not assoc w R - Interim
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.59 ethionamide
hadA 732265 c.336G>A synonymous_variant 0.12 isoniazid Not assoc w R - Interim
nusG 734116 c.-138T>C upstream_gene_variant 0.69 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.26 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.27 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.8 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.69 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.8 rifampicin Not assoc w R
rpoC 765171 p.Pro601Leu missense_variant 0.72 rifampicin Not assoc w R
rpoC 765544 c.2175C>T synonymous_variant 0.75 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 0.97 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776100 p.Thr794Ile missense_variant 0.88 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
rplC 800357 c.-452C>A upstream_gene_variant 0.76 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.84 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.62 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.65 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673283 c.-919A>C upstream_gene_variant 0.68 isoniazid
ethionamide
tsnR 1853974 c.369C>T synonymous_variant 0.71 linezolid Not assoc w R
tlyA 1917777 c.-163A>G upstream_gene_variant 0.57 capreomycin
bacA 2062922 p.Ile603Val missense_variant 0.49 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063847 c.882C>T synonymous_variant 0.65 kanamycin
capreomycin
streptomycin
amikacin
katG 2154724 p.Arg463Leu missense_variant 0.82 isoniazid Not assoc w R
katG 2155557 c.555C>T synonymous_variant 0.58 isoniazid Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.8 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.61 pyrazinamide Uncertain significance
Rv1979c 2221783 p.Ala461Glu missense_variant 0.61 bedaquiline Uncertain significance
clofazimine
Rv1979c 2222308 p.Asp286Gly missense_variant 0.58 bedaquiline Not assoc w R - Interim
clofazimine 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 0.28 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.28 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.56 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.81 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.26 isoniazid Not assoc w R
ahpC 2726672 c.480G>A synonymous_variant 0.62 isoniazid Not assoc w R - Interim
Rv2477c 2782498 c.1545C>T synonymous_variant 0.28 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
Rv2681 2996876 c.138A>C synonymous_variant 0.38 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.59 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
Rv2752c 3064771 p.Ala474Val missense_variant 0.38 levofloxacin
moxifloxacin Uncertain significance
isoniazid Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 0.84 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.74 ethionamide Uncertain significance
whiB7 3569029 c.-350A>G upstream_gene_variant 0.14 kanamycin Not assoc w R
amikacin Uncertain significance
streptomycin Uncertain significance
lpqB 3624486 p.Asp142Gly missense_variant 0.58 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.67 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626360 p.Arg85His missense_variant 0.62 rifampicin
bedaquiline
fbiA 3640279 c.-264T>C upstream_gene_variant 0.6 pretomanid
delamanid
clofazimine
clpC1 4040517 p.Val63Ala missense_variant 0.7 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.39 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
streptomycin Not assoc w R
rifampicin Not assoc w R
ethambutol Not assoc w R
glpK 4138622 c.1134C>T synonymous_variant 0.41 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
glpK 4139670 p.Cys29Tyr missense_variant 0.12 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
embC 4240172 p.Val104Met missense_variant 0.31 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.5 ethambutol Not assoc w R
embC 4241562 p.Arg567His missense_variant 0.33 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.25 ethambutol Not assoc w R
embA 4245166 p.Pro645Gln missense_variant 0.65 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 0.56 ethambutol Not assoc w R
embB 4249439 p.Glu976Lys missense_variant 0.17 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.63 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.51 ethambutol Not assoc w R
ethA 4328329 c.-856C>G upstream_gene_variant 0.14 ethionamide
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 0.62 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 4338846 c.-325T>G upstream_gene_variant 0.19 kanamycin
capreomycin
amikacin
gid 4407588 c.615A>G synonymous_variant 0.81 streptomycin Not assoc w R
gid 4407873 c.330G>T synonymous_variant 0.74 streptomycin Not assoc w R
gid 4407950 p.Asp85Asn missense_variant 0.71 streptomycin Uncertain significance