TB-Profiler result

Run: ERR9992898
Summary

Run ID: ERR9992898

Sample name:

Date: 2024-04-16T07:45:52.862364

Number of reads: 3936872

Percentage reads mapped: 99.63

Median coverage: 121.0

Strain: lineage1.2.2.2;lineage2.2.1

Spoligotype:

Drug-resistance: XDR-TB

Download CSV Download TXT Download JSON
Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.2 Indo-Oceanic RD239 0.16
lineage2 East-Asian RD105 0.82
lineage1.2.2.2 Indo-Oceanic RD239 0.16
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.83
lineage2.2 East-Asian (Beijing) RD105;RD207 0.84
lineage1 Indo-Oceanic RD239 0.17
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 inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
p.Ile194Thr Uncertain significance Mutation from literature
ethambutol embB p.Met306Val Assoc w R
pyrazinamide pncA p.Ser164Pro Assoc w R
p.Gly97Asp Assoc w R
streptomycin rrs n.517C>T Assoc w R
fluoroquinolones
moxifloxacin gyrB p.Glu501Asp Assoc w R Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
ofloxacin
levofloxacin gyrB p.Glu501Asp Assoc w R - Interim
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
p.Ile194Thr Uncertain significance Mutation from literature
ethR p.Ala95Thr Uncertain significance Mutation from literature
clofazimine mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
c.430dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
para-aminosalicylic_acid
delamanid
bedaquiline mmpR5 c.144dupC Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
c.198dupG Assoc w R Can only confer resistance if genetically linked to a functional MmpL5
c.430dupG 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
gyrB 6742 p.Glu501Asp missense_variant 0.76 levofloxacin Assoc w R - Interim
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 1.0 rifampicin Assoc w R
mmpR5 779130 c.144dupC frameshift_variant 0.63 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
mmpR5 779181 c.198dupG frameshift_variant 0.12 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
mmpR5 779417 c.430dupG frameshift_variant 0.13 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
rrs 1472362 n.517C>T non_coding_transcript_exon_variant 0.18 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.84 ethionamide Assoc w R Alias fabG1_c.-15C>T
isoniazid Assoc w R Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance)
inhA 1674782 p.Ile194Thr missense_variant 0.99 ethionamide Uncertain significance Mutation from literature
isoniazid Uncertain significance Mutation from literature
pncA 2288752 p.Ser164Pro missense_variant 0.72 pyrazinamide Assoc w R
pncA 2288952 p.Gly97Asp missense_variant 0.16 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 1.0 ethambutol Assoc w R
ethR 4327831 p.Ala95Thr missense_variant 0.79 ethionamide Uncertain significance Mutation from literature
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 0.26 levofloxacin
moxifloxacin
gyrB 6112 p.Met291Ile missense_variant 0.2 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7268 c.-34C>T upstream_gene_variant 0.24 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 7879 p.Asn193Ser missense_variant 0.25 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 8452 p.Ala384Val missense_variant 0.25 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.14 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 0.18 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.19 isoniazid Not assoc w R
Rv0010c 13699 c.-141A>G upstream_gene_variant 0.29 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 575907 p.Ala187Val missense_variant 0.85 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.8 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.82 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.86 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.2 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.24 rifampicin Not assoc w R
rpoB 761490 p.Val562Met missense_variant 0.81 rifampicin Uncertain significance
rpoB 762731 p.Gln975His missense_variant 0.18 rifampicin Uncertain significance
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763552 c.183C>T synonymous_variant 0.22 rifampicin Not assoc w R
rpoC 763555 c.186C>T synonymous_variant 0.77 rifampicin Not assoc w R - Interim
rpoC 763884 p.Ala172Val missense_variant 0.19 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.18 rifampicin Not assoc w R
rpoC 766707 p.Glu1113Gly missense_variant 0.9 rifampicin Uncertain significance
rpoC 767123 p.Val1252Leu missense_variant 0.14 rifampicin Uncertain significance
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
mmpL5 776182 p.Asp767Asn missense_variant 0.83 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 778979 c.-74G>T upstream_gene_variant 0.74 clofazimine Uncertain significance
bedaquiline Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.8 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
rplC 800357 c.-452C>A upstream_gene_variant 0.18 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
Rv1258c 1406760 c.580_581insC frameshift_variant 0.85 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.26 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.12 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.16 ethambutol
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rpsA 1834177 c.636A>C synonymous_variant 0.9 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.19 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 0.11 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
ndh 2102240 p.Arg268His missense_variant 0.17 ethionamide Uncertain significance
delamanid Uncertain significance
isoniazid Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
PPE35 2168742 p.Gly624Asp missense_variant 0.28 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.19 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
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 0.17 clofazimine Not assoc w R
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.14 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.12 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
Rv3083 3448714 p.Asp71His missense_variant 0.19 ethionamide Uncertain significance
whiB7 3568474 p.Glu69Gly missense_variant 0.79 streptomycin
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.8 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.12 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 0.12 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
mtrB 3626562 p.Pro18Ser missense_variant 0.82 bedaquiline Uncertain significance
rifampicin Not assoc w R
clpC1 4040517 p.Val63Ala missense_variant 0.16 pyrazinamide Not assoc w R - Interim
clpC1 4040719 c.-15A>G upstream_gene_variant 0.17 pyrazinamide Uncertain significance
glpK 4138377 p.Val460Ala missense_variant 0.23 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
embC 4240671 p.Thr270Ile missense_variant 0.23 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.19 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 0.82 ethambutol Not assoc w R
embA 4245670 p.Ala813Gly missense_variant 0.12 ethambutol Not assoc w R - Interim
embA 4245969 p.Pro913Ser missense_variant 0.18 ethambutol Not assoc w R
embB 4246979 p.Gly156Cys missense_variant 0.19 ethambutol Not assoc w R - Interim
embB 4247646 p.Glu378Ala missense_variant 0.17 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.77 ethambutol Not assoc w R
aftB 4267960 p.Val293Met missense_variant 0.16 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 0.18 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.19 ethambutol Not assoc w R
ethA 4326148 c.1326G>T synonymous_variant 0.24 ethionamide Not assoc w R - Interim
ethA 4326439 p.Asn345Lys missense_variant 0.13 ethionamide Uncertain significance
whiB6 4338203 p.Arg107Cys missense_variant 0.17 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338365 p.Cys53Gly missense_variant 0.84 capreomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
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 0.2 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 0.99 streptomycin Not assoc w R
gid 4407848 p.Ala119Thr missense_variant 0.15 streptomycin Uncertain significance
gid 4407873 c.330G>T synonymous_variant 0.14 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.85 streptomycin Not assoc w R