TB-Profiler result

Run: ERR4830361
Summary

Run ID: ERR4830361

Sample name:

Date: 2024-04-16T12:39:35.555062

Number of reads: 3639510

Percentage reads mapped: 98.39

Median coverage: 89.0

Strain: lineage1.2.1.2.1;lineage2.2.1

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1.2.1.2 Indo-Oceanic RD239 0.75
lineage2 East-Asian RD105 0.23
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.22
lineage2.2 East-Asian (Beijing) RD105;RD207 0.23
lineage1 Indo-Oceanic RD239 0.77
lineage1.2.1.2.1 Indo-Oceanic RD239 0.8
lineage1.2.1 Indo-Oceanic RD239 0.8
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin rpoB p.Val170Phe Assoc w R
p.Lys446Gln Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
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)
ethambutol embB p.Asp354Ala Assoc w R
pyrazinamide pncA c.-11A>G Assoc w R
streptomycin rpsL p.Lys88Arg Assoc w R
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide inhA c.-777C>T Assoc w R Alias fabG1_c.-15C>T
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
rpoB 760314 p.Val170Phe missense_variant 0.22 rifampicin Assoc w R
rpoB 761142 p.Lys446Gln missense_variant 0.29 rifampicin Assoc w R - Interim Expert rule: Non-silent variants in RRDR of rpoB
rpsL 781822 p.Lys88Arg missense_variant 0.24 streptomycin Assoc w R
inhA 1673425 c.-777C>T upstream_gene_variant 0.2 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)
ethionamide Assoc w R Alias fabG1_c.-15C>T
pncA 2289252 c.-11A>G upstream_gene_variant 0.27 pyrazinamide Assoc w R
embB 4247574 p.Asp354Ala missense_variant 0.27 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 1302 c.1302C>A synonymous_variant 0.79 isoniazid Not assoc w R
gyrB 6112 p.Met291Ile missense_variant 0.8 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 0.81 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9143 c.1842T>C synonymous_variant 0.74 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9260 c.1959G>C synonymous_variant 0.79 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 13175 c.384T>C synonymous_variant 0.8 isoniazid Not assoc w R
Rv0010c 13298 p.Ile87Met missense_variant 0.82 isoniazid Not assoc w R
Rv0010c 13460 c.99T>C synonymous_variant 0.88 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 575368 c.21T>C synonymous_variant 0.78 ethionamide Not assoc w R - Interim
isoniazid Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.36 ethionamide Not assoc w R
isoniazid Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.16 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Uncertain significance
Rv0565c 657081 c.390G>A synonymous_variant 0.2 ethionamide Not assoc w R - Interim
Rv0565c 657142 p.Arg110His missense_variant 0.15 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.78 ethionamide
nusG 734116 c.-138T>C upstream_gene_variant 0.82 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 1.0 rifampicin Not assoc w R
rpoC 763531 c.162G>C synonymous_variant 0.79 rifampicin Not assoc w R
rpoC 763884 p.Ala172Val missense_variant 0.85 rifampicin Not assoc w R
rpoC 763886 c.517C>A synonymous_variant 0.85 rifampicin Not assoc w R
rpoC 765846 p.Asn826Thr missense_variant 0.23 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 0.17 clofazimine Not assoc w R
bedaquiline Not assoc w R
mmpS5 779615 c.-710C>G upstream_gene_variant 0.19 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 0.73 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 1406312 c.1029T>C synonymous_variant 0.79 streptomycin Not assoc w R
isoniazid Not assoc w R
pyrazinamide Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.2 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417019 p.Cys110Tyr missense_variant 0.82 ethambutol Not assoc w R
embR 1417554 c.-207C>G upstream_gene_variant 0.69 ethambutol
embR 1417793 c.-446C>T upstream_gene_variant 0.74 ethambutol
atpE 1460907 c.-138T>C upstream_gene_variant 0.74 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 0.79 capreomycin Uncertain significance
linezolid Uncertain significance
inhA 1674162 c.-40C>T upstream_gene_variant 0.78 ethionamide Uncertain significance
isoniazid Not assoc w R
rpsA 1834177 c.636A>C synonymous_variant 0.17 pyrazinamide Not assoc w R - Interim
tsnR 1853974 c.369C>T synonymous_variant 0.91 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 2155001 p.Pro371Ser missense_variant 0.23 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Not assoc w R
Rv1979c 2222308 p.Asp286Gly missense_variant 0.81 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
kasA 2518132 c.18C>T synonymous_variant 0.8 isoniazid
kasA 2519048 p.Gly312Ser missense_variant 0.88 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 0.81 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339417 c.300A>G synonymous_variant 0.69 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
Rv3083 3448714 p.Asp71His missense_variant 0.8 ethionamide Uncertain significance
whiB7 3568488 c.191delG frameshift_variant 0.84 streptomycin Uncertain significance
amikacin Uncertain significance
kanamycin Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.22 pyrazinamide Not assoc w R - Interim
lpqB 3624486 p.Asp142Gly missense_variant 0.75 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 3626562 p.Pro18Ser missense_variant 0.35 bedaquiline Uncertain significance
rifampicin Not assoc w R
fbiA 3640557 c.15T>C synonymous_variant 0.73 clofazimine Not assoc w R - Interim
pretomanid
delamanid Not assoc w R - Interim
clpC1 4040517 p.Val63Ala missense_variant 0.83 pyrazinamide Not assoc w R - Interim
glpK 4138377 p.Val460Ala missense_variant 0.77 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 0.83 ethambutol Not assoc w R
embC 4241042 p.Asn394Asp missense_variant 0.79 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 0.15 ethambutol Not assoc w R
embA 4243580 c.348G>A synonymous_variant 0.76 ethambutol Not assoc w R
embA 4243694 c.462T>C synonymous_variant 0.14 ethambutol
embA 4244420 c.1188G>C synonymous_variant 0.93 ethambutol Not assoc w R
embA 4245969 p.Pro913Ser missense_variant 0.63 ethambutol Not assoc w R
embB 4247578 c.1065G>A synonymous_variant 0.73 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.88 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.14 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.77 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.75 ethambutol Not assoc w R
ubiA 4269864 c.-32delG upstream_gene_variant 0.81 ethambutol Not assoc w R
ethA 4327085 p.Thr130Asn missense_variant 0.23 ethionamide
whiB6 4338361 p.Arg54Gln missense_variant 0.79 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 0.79 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 4407873 c.330G>T synonymous_variant 0.83 streptomycin Not assoc w R
gid 4407927 p.Glu92Asp missense_variant 0.18 streptomycin Not assoc w R