TB-Profiler result

Run: ERR2516985
Summary

Run ID: ERR2516985

Sample name:

Date: 2024-10-04T06:56:47.347985

Number of reads: 4687411

Percentage reads mapped: 99.7

Median coverage: 156.0

Strain: lineage2.2.1.1;lineage4.6.2.2

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4.6 Euro-American None 0.85
lineage2 East-Asian RD105 0.16
lineage4.6.2 Euro-American RD726 0.88
lineage4.6.2.2 Euro-American (Cameroon) RD726 0.85
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 0.14
lineage2.2 East-Asian (Beijing) RD105;RD207 0.13
lineage4 Euro-American None 0.84
lineage2.2.1.1 East-Asian (Beijing) RD105;RD207;RD181;RD150 0.14
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
p.Gly406Ala Assoc w R
pyrazinamide pncA c.390_391dupGG Assoc w R
p.His57Asp Assoc w R
streptomycin rpsL p.Lys43Arg Assoc w R
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
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781687 p.Lys43Arg missense_variant 1.0 streptomycin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R High-level resistance
pncA 2288850 c.390_391dupGG frameshift_variant 0.12 pyrazinamide Assoc w R
pncA 2289073 p.His57Asp missense_variant 0.9 pyrazinamide Assoc w R
embB 4247429 p.Met306Val missense_variant 0.15 ethambutol Assoc w R
embB 4247730 p.Gly406Ala missense_variant 0.84 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
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 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
mshA 575907 p.Ala187Val missense_variant 0.18 isoniazid Not assoc w R
ethionamide Not assoc w R
ccsA 620625 p.Ile245Met missense_variant 0.22 kanamycin Uncertain significance
capreomycin Not assoc w R
amikacin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.11 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 0.16 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
mmpL5 776182 p.Asp767Asn missense_variant 0.17 bedaquiline Not assoc w R
clofazimine Not assoc w R
mmpL5 778298 c.183G>A synonymous_variant 0.88 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R - Interim
mmpS5 779615 c.-710C>G upstream_gene_variant 0.12 bedaquiline
clofazimine
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1258c 1406760 c.580_581insC frameshift_variant 0.18 streptomycin Uncertain significance
pyrazinamide Uncertain significance
isoniazid Uncertain significance
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 kanamycin
capreomycin
streptomycin
amikacin
inhA 1673393 c.-809G>C upstream_gene_variant 0.93 isoniazid Uncertain significance
ethionamide Uncertain significance
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 2063096 p.Arg545Cys missense_variant 0.85 kanamycin Uncertain significance
capreomycin
streptomycin
amikacin
bacA 2063187 c.1542C>T synonymous_variant 0.82 kanamycin Not assoc w R
capreomycin Not assoc w R - Interim
streptomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
PPE35 2167926 p.Leu896Ser missense_variant 0.13 pyrazinamide Not assoc w R
Rv1979c 2221746 c.1416_1418dupCCG disruptive_inframe_insertion 0.93 bedaquiline Uncertain significance
clofazimine Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 bedaquiline Not assoc w R - Interim
clofazimine Not assoc w R
eis 2714846 p.Val163Ile missense_variant 0.15 kanamycin Not assoc w R
amikacin Not assoc w R
folC 2746320 p.Pro427Ala missense_variant 0.77 para-aminosalicylic_acid
Rv2680 2996208 p.Ala35Asp missense_variant 0.74 capreomycin Uncertain significance
Rv3083 3448567 p.His22Asp missense_variant 0.85 ethionamide Uncertain significance
Rv3236c 3612813 p.Thr102Ala missense_variant 0.2 pyrazinamide Not assoc w R - Interim
mtrB 3625065 p.Met517Leu missense_variant 0.15 rifampicin Not assoc w R
bedaquiline Uncertain significance
mtrB 3626562 p.Pro18Ser missense_variant 0.13 rifampicin Not assoc w R
bedaquiline Uncertain significance
ddn 3987011 c.168C>T synonymous_variant 0.89 pretomanid
delamanid Not assoc w R - Interim
glpK 4139183 c.572dupG frameshift_variant 0.37 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
isoniazid Uncertain significance
streptomycin Uncertain significance
rifampicin Uncertain significance
ethambutol Uncertain significance
glpK 4139607 p.Leu50Pro missense_variant 0.42 levofloxacin
moxifloxacin
isoniazid
streptomycin
rifampicin
ethambutol
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embA 4243460 c.228C>T synonymous_variant 0.26 ethambutol Not assoc w R
embB 4247880 p.Val456Ala missense_variant 0.15 ethambutol Uncertain significance
embB 4248115 c.1602C>T synonymous_variant 0.12 ethambutol Not assoc w R
aftB 4267272 p.Lys522Arg missense_variant 0.86 ethambutol Not assoc w R
aftB 4267647 p.Asp397Gly missense_variant 0.16 ethambutol Not assoc w R
ubiA 4269121 p.Phe238Ser missense_variant 0.88 ethambutol Uncertain significance
ethA 4326632 p.His281Arg missense_variant 0.89 ethionamide Uncertain significance
ethA 4326739 c.735C>G synonymous_variant 0.9 ethionamide Not assoc w R - Interim
ethR 4328004 c.456G>A synonymous_variant 0.91 ethionamide Not assoc w R - Interim
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 4407927 p.Glu92Asp missense_variant 0.11 streptomycin Not assoc w R