TB-Profiler result

Run: SRR25827489
Summary

Run ID: SRR25827489

Sample name:

Date: 2024-10-04T18:36:07.816184

Number of reads: 8079688

Percentage reads mapped: 95.89

Median coverage: 278.0

Strain: lineage1.1.2;lineage2.2.1;lineage3.1.2.1

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 0.58
lineage1.1.2 Indo-Oceanic RD239 0.15
lineage3.1.2 East-African-Indian RD750 0.58
lineage2 East-Asian RD105 0.25
lineage1.1 Indo-Oceanic RD239 0.18
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.24
lineage2.2 East-Asian (Beijing) RD105;RD207 0.23
lineage1 Indo-Oceanic RD239 0.15
lineage3.1.2.1 East-African-Indian RD750 0.6
lineage3.1 East-African-Indian RD750 0.59
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
isoniazid katG p.Ser315Thr Assoc w R High-level resistance
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Leu159Arg Assoc w R
p.Asp12Ala Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
fluoroquinolones
moxifloxacin gyrA p.Asp94Gly Assoc w R High-level resistance
ofloxacin
levofloxacin gyrA p.Asp94Gly Assoc w R
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine mmpR5 c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
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
gyrA 7582 p.Asp94Gly missense_variant 0.58 levofloxacin Assoc w R
moxifloxacin Assoc w R High-level resistance
rpoB 761155 p.Ser450Leu missense_variant 0.83 rifampicin Assoc w R
mmpR5 779181 c.198dupG frameshift_variant 0.18 bedaquiline Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
clofazimine Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
rpsL 781687 p.Lys43Arg missense_variant 0.79 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 0.84 isoniazid Assoc w R High-level resistance
pncA 2288766 p.Leu159Arg missense_variant 0.25 pyrazinamide Assoc w R
pncA 2289207 p.Asp12Ala missense_variant 0.64 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.23 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
gyrB 6112 p.Met291Ile missense_variant 0.19 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrB 6124 c.885C>T synonymous_variant 0.19 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 0.2 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 0.16 isoniazid Not assoc w R
fgd1 491290 p.Val170Met missense_variant 0.38 pretomanid
delamanid Uncertain significance
clofazimine 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
mshA 575907 p.Ala187Val missense_variant 0.23 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 619968 c.78G>A synonymous_variant 0.62 kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
ccsA 620625 p.Ile245Met missense_variant 0.25 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
Rv0565c 657081 c.390G>A synonymous_variant 0.85 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.25 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.21 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.18 rifampicin Not assoc w R
nusG 734133 c.-121G>C upstream_gene_variant 0.17 rifampicin Uncertain significance
rpoB 759546 c.-261A>G upstream_gene_variant 0.2 rifampicin Not assoc w R
rpoB 759746 c.-61C>T upstream_gene_variant 0.69 rifampicin Not assoc w R
rpoB 762434 c.2628T>G synonymous_variant 0.59 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 0.18 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 764916 p.Leu516Pro missense_variant 0.52 rifampicin Uncertain significance
rpoC 765171 p.Pro601Leu missense_variant 0.21 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
mmpL5 776182 p.Asp767Asn missense_variant 0.29 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 776395 p.Phe696Leu missense_variant 0.15 bedaquiline Uncertain significance
clofazimine Not assoc w R
mmpS5 778883 p.Ala8Val missense_variant 0.17 bedaquiline Uncertain significance
clofazimine Uncertain significance
mmpS5 779615 c.-710C>G upstream_gene_variant 0.24 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800131 c.-678A>G upstream_gene_variant 0.64 linezolid
Rv1129c 1253930 p.Phe202Tyr missense_variant 0.24 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
fbiC 1303953 c.1023C>T synonymous_variant 0.17 pretomanid
delamanid Not assoc w R - Interim
clofazimine Not assoc w R - Interim
Rv1258c 1406760 c.580_581insC frameshift_variant 0.18 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
Rv1258c 1406878 p.Ile155Val missense_variant 0.21 streptomycin
pyrazinamide
isoniazid
embR 1417236 p.Val38Met missense_variant 0.2 ethambutol Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.15 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.29 pyrazinamide Not assoc w R - Interim
tsnR 1854045 p.Tyr147Cys missense_variant 0.17 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 0.17 kanamycin Not assoc w R
capreomycin Not assoc w R
streptomycin Not assoc w R
amikacin Not assoc w R
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
katG 2156752 c.-641A>G upstream_gene_variant 0.58 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168604 p.Pro670Leu missense_variant 0.55 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 0.52 pyrazinamide Not assoc w R
pncA 2289365 c.-125delC upstream_gene_variant 0.57 pyrazinamide
ahpC 2726051 c.-142G>A upstream_gene_variant 0.18 isoniazid
ahpC 2726105 c.-88G>A upstream_gene_variant 0.59 isoniazid Not assoc w R
Rv2477c 2782498 c.1545C>T synonymous_variant 0.6 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 2783920 c.123G>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783929 c.114C>G synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783932 c.111C>T synonymous_variant 0.17 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2783938 c.105T>C synonymous_variant 0.16 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2477c 2784499 c.-457G>A upstream_gene_variant 0.21 kanamycin
levofloxacin
moxifloxacin
streptomycin
rifampicin
ethambutol
amikacin
Rv2681 2996912 c.174C>T synonymous_variant 0.21 capreomycin Not assoc w R
Rv2752c 3064632 c.1560C>T synonymous_variant 0.18 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 3448554 c.51C>T synonymous_variant 0.58 ethionamide
Rv3083 3448714 p.Asp71His missense_variant 0.17 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.29 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 1.0 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626467 c.147G>A synonymous_variant 0.22 rifampicin Not assoc w R
bedaquiline Not assoc w R - Interim
mtrB 3626562 p.Pro18Ser missense_variant 0.19 rifampicin Not assoc w R
bedaquiline Uncertain significance
rpoA 3878416 p.Gly31Ala missense_variant 0.27 rifampicin Uncertain significance
clpC1 4040517 p.Val63Ala missense_variant 0.16 pyrazinamide Not assoc w R - Interim
panD 4044872 c.-591C>T upstream_gene_variant 0.57 pyrazinamide
glpK 4138377 p.Val460Ala missense_variant 0.21 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 0.56 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 0.24 ethambutol Not assoc w R
embC 4241022 p.Ala387Val missense_variant 0.24 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 0.17 ethambutol Not assoc w R
embC 4242075 p.Arg738Gln missense_variant 0.57 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243192 c.-40delT upstream_gene_variant 0.63 ethambutol Uncertain significance
embA 4243460 c.228C>T synonymous_variant 0.27 ethambutol Not assoc w R
embA 4243848 p.Val206Met missense_variant 0.18 ethambutol Not assoc w R
embA 4244515 p.Ala428Val missense_variant 0.59 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.18 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.2 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 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 4407620 p.Tyr195His missense_variant 0.21 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.26 streptomycin Not assoc w R