TB-Profiler result

Run: SRR25827357
Summary

Run ID: SRR25827357

Sample name:

Date: 2024-10-05T08:02:40.296371

Number of reads: 11680898

Percentage reads mapped: 99.05

Median coverage: 355.0

Strain: lineage1.1.2;lineage2.2.1;lineage3

Spoligotype:

Drug-resistance: 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 0.15
lineage1.1.2 Indo-Oceanic RD239 0.43
lineage2 East-Asian RD105 0.28
lineage1.1 Indo-Oceanic RD239 0.43
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.26
lineage2.2 East-Asian (Beijing) RD105;RD207 0.3
lineage1 Indo-Oceanic RD239 0.43
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Ser450Leu Assoc w R
p.Ile480Val Uncertain significance Mutation from literature
p.Ile491Phe Assoc w R
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
p.Gln497Arg Assoc w R
pyrazinamide pncA p.Pro54Ser Assoc w R - Interim
streptomycin rpsL p.Lys43Arg Assoc w R
p.Lys88Thr Uncertain significance Mutation from literature
fluoroquinolones
moxifloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Ser91Pro Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Thr500Asn Uncertain significance Mutation from literature
gyrA p.Ser91Pro Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin eis c.-10G>A Assoc w R Can only confer resistance if genetically linked to a functional Eis
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid rplC p.Cys154Arg Assoc w R
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 6738 p.Thr500Asn missense_variant 0.42 levofloxacin Uncertain significance Mutation from literature
moxifloxacin Uncertain significance Mutation from literature
gyrA 7572 p.Ser91Pro missense_variant 0.15 levofloxacin Assoc w R
moxifloxacin Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
rpoB 761155 p.Ser450Leu missense_variant 0.61 rifampicin Assoc w R
rpoB 761244 p.Ile480Val missense_variant 0.45 rifampicin Uncertain significance Mutation from literature
rpoB 761277 p.Ile491Phe missense_variant 0.41 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 0.41 streptomycin Assoc w R
rpsL 781822 p.Lys88Thr missense_variant 0.18 streptomycin Uncertain significance Mutation from literature
rplC 801268 p.Cys154Arg missense_variant 0.38 linezolid Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.99 isoniazid Assoc w R High-level resistance
pncA 2289082 p.Pro54Ser missense_variant 0.42 pyrazinamide Assoc w R - Interim
eis 2715342 c.-10G>A upstream_gene_variant 0.46 kanamycin Assoc w R Can only confer resistance if genetically linked to a functional Eis
embB 4247429 p.Met306Val missense_variant 0.17 ethambutol Assoc w R
embB 4248003 p.Gln497Arg missense_variant 0.5 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
dnaA 1288 p.Glu430Lys missense_variant 0.36 isoniazid Uncertain significance
dnaA 1519 p.Arg507Cys missense_variant 0.5 isoniazid Uncertain significance
gyrB 6112 p.Met291Ile missense_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.43 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6736 c.1497C>T synonymous_variant 0.42 levofloxacin Not assoc w R - Interim
moxifloxacin Not assoc w R - Interim
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 0.45 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.42 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 0.44 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.18 pretomanid
delamanid Uncertain significance
clofazimine Not assoc w R
fgd1 491742 c.960T>C synonymous_variant 0.9 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.24 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620553 c.663T>C synonymous_variant 0.15 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.32 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.42 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.28 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.42 ethionamide
hadA 732044 p.Tyr39Asn missense_variant 0.36 isoniazid Uncertain significance
nusG 734116 c.-138T>C upstream_gene_variant 0.38 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.17 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.15 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.87 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.37 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.37 rifampicin Not assoc w R
rpoC 764817 p.Val483Ala missense_variant 0.13 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.46 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 0.86 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.25 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.28 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.45 linezolid Not assoc w R
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.88 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
isoniazid Not assoc w R
rifampicin Not assoc w R
Rv1258c 1406503 p.Val280Leu missense_variant 0.42 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406760 c.580_581insC frameshift_variant 0.27 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.45 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.39 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.4 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.26 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.46 linezolid Not assoc w R
tsnR 1854045 p.Tyr147Cys missense_variant 0.46 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 0.4 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
bacA 2063075 c.1651_1653dupCTC conservative_inframe_insertion 0.4 kanamycin
capreomycin
streptomycin
amikacin
ndh 2102072 c.969_970dupGG frameshift_variant 0.37 isoniazid Uncertain significance
delamanid Uncertain significance
ethionamide Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.84 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.85 pyrazinamide Not assoc w R
PPE35 2167983 p.Gly877Asp missense_variant 0.38 pyrazinamide Uncertain significance
PPE35 2168565 p.Pro683Leu missense_variant 0.16 pyrazinamide Uncertain significance
PPE35 2170599 p.Val5Ala missense_variant 0.19 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.38 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 0.18 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.15 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 0.54 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.39 isoniazid
Rv2477c 2782498 c.1545C>T synonymous_variant 0.17 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
Rv2477c 2784211 c.-169A>C upstream_gene_variant 0.18 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
ribD 2986827 c.-12G>A upstream_gene_variant 0.27 para-aminosalicylic_acid
Rv2681 2996912 c.174C>T synonymous_variant 0.4 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.42 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
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.4 ethionamide Uncertain significance
whiB7 3568425 c.255T>G synonymous_variant 0.16 kanamycin
amikacin
streptomycin
Rv3236c 3612813 p.Thr102Ala missense_variant 0.29 pyrazinamide Not assoc w R - Interim
Rv3236c 3613710 c.-594G>T upstream_gene_variant 0.17 pyrazinamide
lpqB 3624486 p.Asp142Gly missense_variant 0.44 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3625065 p.Met517Leu missense_variant 0.99 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.26 rifampicin Not assoc w R
bedaquiline Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.49 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.15 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.38 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 0.15 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 4240671 p.Thr270Ile missense_variant 0.47 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.19 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.37 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.27 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.44 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.4 ethambutol Not assoc w R
embB 4246563 p.Leu17Trp missense_variant 0.54 ethambutol Uncertain significance
embB 4246567 c.54G>T synonymous_variant 0.59 ethambutol Not assoc w R - Interim
embB 4247028 p.Leu172Arg missense_variant 0.15 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.42 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.21 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.45 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.4 ethambutol Not assoc w R
whiB6 4338224 c.297delC frameshift_variant 0.43 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 0.39 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 0.88 streptomycin Not assoc w R
gid 4407714 p.Lys163Asn missense_variant 0.48 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.43 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.3 streptomycin Not assoc w R