TB-Profiler result

Run: 76b1ac41-2c15-47b0-b35d-ea90f2ee2e48
Summary

Run ID: 76b1ac41-2c15-47b0-b35d-ea90f2ee2e48

Sample name:

Date: 01-04-2024 12:02:37

Number of reads: 597697

Percentage reads mapped: 97.98

Median coverage: 14

Strain: lineage2.2.1

Spoligotype:

Drug-resistance: Pre-XDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage2 East-Asian RD105 1.0
lineage2.2 East-Asian (Beijing) RD105;RD207 1.0
lineage2.2.1 East-Asian (Beijing) RD105;RD207;RD181 1.0
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 fabG1 c.-15C>T Assoc w R
katG p.Ser315Thr Assoc w R
ethambutol embA c.-12C>T Assoc w R
embB p.Tyr334His Uncertain significance
pyrazinamide pncA p.Tyr103* Assoc w R
moxifloxacin gyrA p.Asp94Gly Assoc w R
levofloxacin gyrA p.Asp94Gly Assoc w R
bedaquiline
delamanid
pretomanid
linezolid
streptomycin rpsL p.Lys88Arg Assoc w R
amikacin
kanamycin eis c.-12C>T Assoc w R
capreomycin
clofazimine
ethionamide fabG1 c.-15C>T Assoc w R
para-aminosalicylic_acid
cycloserine
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 1.0 ofloxacin Uncertain significance
moxifloxacin Assoc w R
levofloxacin Assoc w R
fluoroquinolones Uncertain significance
ciprofloxacin Uncertain significance
rpoB 761155 p.Ser450Leu missense_variant 1.0 rifampicin Assoc w R
rpsL 781822 p.Lys88Arg missense_variant 1.0 streptomycin Assoc w R
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid Assoc w R
ethionamide Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R
pncA 2288933 p.Tyr103* stop_gained 1.0 pyrazinamide Assoc w R
eis 2715344 c.-12C>T upstream_gene_variant 1.0 kanamycin Assoc w R
embA 4243221 c.-12C>T upstream_gene_variant 1.0 ethambutol Assoc w R
embB 4247513 p.Tyr334His missense_variant 0.82 ethambutol Uncertain significance
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 5488 c.249C>T synonymous_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 7585 p.Ser95Thr missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
mshA 575907 p.Ala187Val missense_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
ccsA 620266 p.Ala126Thr missense_variant 0.12 capreomycin
amikacin
ccsA 620625 p.Ile245Met missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 764817 p.Val483Gly missense_variant 1.0 rifampicin
rpoC 764869 c.1500C>T synonymous_variant 0.1 rifampicin
rpoC 765702 p.Trp778* stop_gained 0.12 rifampicin
rpoC 766645 p.Glu1092Asp missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 775817 c.2664T>C synonymous_variant 0.16 clofazimine
bedaquiline
mmpL5 775826 c.2655G>C synonymous_variant 0.11 clofazimine
bedaquiline
mmpL5 775871 c.2610C>T synonymous_variant 0.1 clofazimine
bedaquiline
mmpL5 775874 c.2607C>A synonymous_variant 0.11 clofazimine
bedaquiline
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776137 p.Ser782Ala missense_variant 0.13 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776138 c.2343C>A synonymous_variant 0.13 clofazimine
bedaquiline
mmpL5 776182 p.Asp767Asn missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 777119 p.His454Gln missense_variant 0.31 clofazimine Uncertain significance
bedaquiline
mmpL5 777122 c.1359C>T synonymous_variant 0.3 clofazimine
bedaquiline
mmpL5 777128 c.1353A>G synonymous_variant 0.31 clofazimine
bedaquiline
mmpR5 778082 c.-908T>C upstream_gene_variant 0.2 clofazimine
bedaquiline
mmpR5 778088 c.-902C>G upstream_gene_variant 0.2 clofazimine
bedaquiline
mmpS5 778703 p.Asn68Ser missense_variant 0.12 clofazimine
bedaquiline
mmpR5 779242 p.Val85Phe missense_variant 0.2 clofazimine
bedaquiline
mmpS5 779615 c.-710C>G upstream_gene_variant 1.0 clofazimine
bedaquiline
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1303016 p.Val29Gly missense_variant 0.36 delamanid
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1473484 n.-174C>A upstream_gene_variant 0.12 linezolid
fabG1 1673380 c.-60C>G upstream_gene_variant 0.48 ethionamide
isoniazid
inhA 1674214 c.13C>T synonymous_variant 0.12 ethionamide
isoniazid
rpsA 1834177 c.636A>C synonymous_variant 1.0 pyrazinamide
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
ndh 2102389 c.654G>C synonymous_variant 0.12 ethionamide
isoniazid
ndh 2102392 c.651C>A synonymous_variant 0.12 ethionamide
isoniazid
ndh 2102401 c.642T>C synonymous_variant 0.12 ethionamide
isoniazid
ndh 2102875 c.168C>T synonymous_variant 0.12 ethionamide
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
katG 2155231 p.Glu294Val missense_variant 0.13 isoniazid
katG 2156010 c.102A>G synonymous_variant 0.11 isoniazid
PPE35 2167745 p.Thr956Arg missense_variant 0.2 pyrazinamide
PPE35 2167865 c.2748G>C synonymous_variant 0.12 pyrazinamide
PPE35 2167868 c.2745A>C synonymous_variant 0.12 pyrazinamide
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2167965 p.Ala883Gly missense_variant 0.29 pyrazinamide
PPE35 2167967 c.2646A>C synonymous_variant 0.29 pyrazinamide
PPE35 2169278 c.1335T>C synonymous_variant 0.16 pyrazinamide
PPE35 2169281 c.1332T>G synonymous_variant 0.15 pyrazinamide
PPE35 2169386 c.1227C>A synonymous_variant 0.13 pyrazinamide
PPE35 2169394 p.Ala407Ser missense_variant 0.13 pyrazinamide
PPE35 2169602 c.1011C>A synonymous_variant 0.1 pyrazinamide
PPE35 2169671 c.942C>G synonymous_variant 0.13 pyrazinamide
PPE35 2169674 c.939T>C synonymous_variant 0.12 pyrazinamide
PPE35 2169677 c.936C>G synonymous_variant 0.12 pyrazinamide
PPE35 2169686 c.927T>C synonymous_variant 0.15 pyrazinamide
PPE35 2169689 c.924C>A synonymous_variant 0.15 pyrazinamide
PPE35 2169902 p.Leu237Phe missense_variant 0.15 pyrazinamide
PPE35 2169910 p.Asn235Tyr missense_variant 0.14 pyrazinamide
PPE35 2169974 c.639T>C synonymous_variant 0.17 pyrazinamide
PPE35 2170406 c.207A>G synonymous_variant 0.11 pyrazinamide
PPE35 2170528 p.Ser29Ala missense_variant 0.11 pyrazinamide
Rv1979c 2222244 c.921A>C synonymous_variant 0.1 clofazimine
bedaquiline
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
kasA 2518236 p.Ser41Ile missense_variant 0.13 isoniazid
kasA 2518809 p.Lys232Arg missense_variant 0.15 isoniazid
kasA 2518864 c.750G>C synonymous_variant 0.19 isoniazid
kasA 2518879 c.765A>G synonymous_variant 0.22 isoniazid
kasA 2518882 c.768C>A synonymous_variant 0.22 isoniazid
kasA 2519140 c.1026G>C synonymous_variant 0.21 isoniazid
kasA 2519143 c.1029G>C synonymous_variant 0.19 isoniazid
kasA 2519153 p.Ile347Val missense_variant 0.13 isoniazid
ahpC 2726493 p.Asn101Asp missense_variant 0.17 isoniazid
Rv2752c 3065742 c.450T>C synonymous_variant 0.17 rifampicin
isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087532 p.Ala238Asp missense_variant 1.0 cycloserine
Rv3083 3448911 c.408C>T synonymous_variant 0.17 ethionamide
Rv3083 3449049 c.546C>G synonymous_variant 0.13 ethionamide
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
Rv3236c 3612229 c.888C>T synonymous_variant 1.0 pyrazinamide
Rv3236c 3612813 p.Thr102Ala missense_variant 1.0 pyrazinamide Uncertain significance
fbiB 3641803 p.Asp90Val missense_variant 0.12 delamanid
alr 3841546 c.-126C>A upstream_gene_variant 0.18 cycloserine
clpC1 4039003 p.Asn568Asp missense_variant 0.17 pyrazinamide
clpC1 4039169 p.Glu512Asp missense_variant 0.12 pyrazinamide
clpC1 4039714 p.Tyr331His missense_variant 0.1 pyrazinamide
clpC1 4039730 c.975C>G synonymous_variant 0.1 pyrazinamide
clpC1 4040001 p.His235Ala missense_variant 0.15 pyrazinamide
clpC1 4040010 p.Ala232Arg missense_variant 0.14 pyrazinamide
embC 4240801 c.939C>T synonymous_variant 0.23 ethambutol
embC 4240803 p.Tyr314Phe missense_variant 0.23 ethambutol
embC 4241427 p.Leu522Gln missense_variant 0.12 ethambutol
embC 4241970 p.Ile703Thr missense_variant 0.12 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4243460 c.228C>T synonymous_variant 1.0 ethambutol
embA 4244210 c.978G>A synonymous_variant 0.12 ethambutol
embA 4244214 p.Ala328Thr missense_variant 0.12 ethambutol
embA 4244515 p.Ala428Val missense_variant 0.11 ethambutol Uncertain significance
embB 4247445 p.Asp311Val missense_variant 0.1 ethambutol
embB 4247512 c.999T>C synonymous_variant 0.18 ethambutol
embB 4247516 p.Asn335Asp missense_variant 0.18 ethambutol
embB 4249029 p.Pro839Leu missense_variant 0.12 ethambutol
embB 4249323 p.Ala937Glu missense_variant 0.27 ethambutol
ethR 4327369 c.-180C>A upstream_gene_variant 0.18 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 1.0 streptomycin
gid 4407927 p.Glu92Asp missense_variant 1.0 streptomycin Uncertain significance