TB-Profiler result

Run: 6b4e926b-4300-42ae-adb5-5a12f2f92507
Summary

Run ID: 6b4e926b-4300-42ae-adb5-5a12f2f92507

Sample name:

Date: 29-03-2024 09:39:06

Number of reads: 2611733

Percentage reads mapped: 92.74

Median coverage: 89

Strain: lineage1.1.2

Spoligotype:

Drug-resistance: HR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage1 Indo-Oceanic RD239 0.99
lineage1.1 Indo-Oceanic RD239 1.0
lineage1.1.2 Indo-Oceanic RD239 0.99
Drug resistance: This table reports drug-resistance associated mutations found in known resistance genes
Drug Resistance Supporting mutations WHO confidence Comment
rifampicin
isoniazid fabG1 c.-15C>T Assoc w R
ethambutol
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
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
fabG1 1673425 c.-15C>T upstream_gene_variant 1.0 isoniazid Assoc w R
ethionamide 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 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrB 6124 c.885C>T synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6860 p.Ser541Pro missense_variant 0.11 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6880 p.Leu547Phe missense_variant 0.16 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 6889 c.-413G>T upstream_gene_variant 0.12 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6913 p.Asn558Lys missense_variant 0.13 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 6922 c.-380G>T upstream_gene_variant 0.32 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6932 p.Gln565Lys missense_variant 0.17 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 8452 p.Ala384Val missense_variant 0.99 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9047 c.1746C>T synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9143 c.1842T>C synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 0.99 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9443 c.2142G>A synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
fgd1 490751 c.-32T>G upstream_gene_variant 0.16 delamanid
fgd1 490759 c.-24A>T upstream_gene_variant 0.2 delamanid
fgd1 490763 c.-20C>G upstream_gene_variant 0.14 delamanid
fgd1 490771 c.-12T>G upstream_gene_variant 0.2 delamanid
fgd1 490780 c.-3C>A upstream_gene_variant 0.16 delamanid
fgd1 490787 p.Ala2Gly missense_variant 0.19 delamanid
fgd1 490790 p.Glu3Gly missense_variant 0.15 delamanid
fgd1 490803 c.21T>G synonymous_variant 0.12 delamanid
fgd1 490810 p.Ala10Thr missense_variant 0.15 delamanid
fgd1 491014 p.Thr78Pro missense_variant 0.17 delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
mshA 575176 c.-172T>G upstream_gene_variant 0.17 ethionamide
isoniazid
mshA 575873 p.Thr176Pro missense_variant 0.13 ethionamide
isoniazid
mshA 575976 p.Ala210Gly missense_variant 0.11 ethionamide
isoniazid
mshA 576000 p.Asp218Ala missense_variant 0.99 ethionamide Uncertain significance
isoniazid Uncertain significance
mshA 576718 c.1371C>G synonymous_variant 0.13 ethionamide
isoniazid
mshA 576732 p.Asp462Ala missense_variant 0.16 ethionamide
isoniazid
mshA 576739 c.1392A>G synonymous_variant 0.12 ethionamide
isoniazid
mshA 576741 p.Ala465Gly missense_variant 0.15 ethionamide
isoniazid
mshA 576744 p.Val466Gly missense_variant 0.12 ethionamide
isoniazid
ccsA 619831 c.-60T>G upstream_gene_variant 0.14 capreomycin
amikacin
ccsA 620551 p.Asp221His missense_variant 0.22 capreomycin
amikacin
ccsA 620558 p.Gln223Pro missense_variant 0.14 capreomycin
amikacin
ccsA 620561 p.Thr224Asn missense_variant 0.12 capreomycin
amikacin
ccsA 620564 p.Leu225Pro missense_variant 0.12 capreomycin
amikacin
ccsA 620567 p.Asp226Gly missense_variant 0.17 capreomycin
amikacin
ccsA 620571 c.681A>G synonymous_variant 0.12 capreomycin
amikacin
ccsA 620748 c.858T>G synonymous_variant 0.16 capreomycin
amikacin
ccsA 620752 p.Arg288Gly missense_variant 0.13 capreomycin
amikacin
ccsA 620756 p.Asp289Gly missense_variant 0.2 capreomycin
amikacin
ccsA 620773 p.Ile295Val missense_variant 0.2 capreomycin
amikacin
rpoB 759611 c.-196G>C upstream_gene_variant 0.22 rifampicin
rpoB 759615 c.-192A>C upstream_gene_variant 0.33 rifampicin
rpoB 759620 c.-187A>C upstream_gene_variant 0.37 rifampicin
rpoB 760490 c.684C>T synonymous_variant 0.99 rifampicin
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 763884 p.Ala172Val missense_variant 0.99 rifampicin Uncertain significance
rpoC 763886 c.517C>A synonymous_variant 0.99 rifampicin
rpoC 765171 p.Pro601Leu missense_variant 1.0 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776395 p.Phe696Leu missense_variant 0.99 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781363 c.-197T>G upstream_gene_variant 0.19 streptomycin
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rplC 801287 p.Val160Gly missense_variant 0.13 linezolid
fbiC 1303016 p.Val29Gly missense_variant 0.16 delamanid
fbiC 1304159 p.Val410Gly missense_variant 0.13 delamanid
fbiC 1304166 c.1236A>G synonymous_variant 0.14 delamanid
Rv1258c 1407039 p.Val101Gly missense_variant 0.16 streptomycin
pyrazinamide
isoniazid
Rv1258c 1407045 p.Asp99Gly missense_variant 0.13 streptomycin
pyrazinamide
isoniazid
Rv1258c 1407055 p.Tyr96Asp missense_variant 0.18 streptomycin
pyrazinamide
isoniazid
embR 1417019 p.Cys110Tyr missense_variant 0.99 ethambutol Uncertain significance
atpE 1461101 c.57T>G synonymous_variant 0.14 bedaquiline
atpE 1461131 c.87T>G synonymous_variant 0.14 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
ndh 2102497 c.546T>G synonymous_variant 0.19 ethionamide
isoniazid
ndh 2102502 p.Thr181Pro missense_variant 0.13 ethionamide
isoniazid
ndh 2102510 p.Ala178Gly missense_variant 0.16 ethionamide
isoniazid
ndh 2102524 c.519C>T synonymous_variant 0.16 ethionamide
isoniazid
ndh 2103225 c.-183A>C upstream_gene_variant 0.25 ethionamide
isoniazid
ndh 2103235 c.-193C>G upstream_gene_variant 0.11 ethionamide
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
katG 2156186 c.-75A>G upstream_gene_variant 1.0 isoniazid
PPE35 2167660 p.Thr985Pro missense_variant 0.12 pyrazinamide
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2167983 p.Gly877Asp missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2169317 c.1296C>T synonymous_variant 0.13 pyrazinamide
PPE35 2169369 p.Gly415Ala missense_variant 1.0 pyrazinamide
PPE35 2170082 c.531T>G synonymous_variant 0.12 pyrazinamide
PPE35 2170338 p.Val92Gly missense_variant 0.11 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
kasA 2518147 c.33C>T synonymous_variant 0.17 isoniazid
kasA 2518161 p.Val16Gly missense_variant 0.12 isoniazid
eis 2714549 p.Met262Leu missense_variant 0.24 kanamycin
amikacin
eis 2714561 p.Gly258Cys missense_variant 0.16 kanamycin
amikacin
eis 2714566 p.Leu256Pro missense_variant 0.29 kanamycin Uncertain significance
amikacin
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
ahpC 2726269 p.Val26Gly missense_variant 0.12 isoniazid
ahpC 2726338 p.Val49Gly missense_variant 0.25 isoniazid
ahpC 2726341 p.Val50Gly missense_variant 0.29 isoniazid
ahpC 2726345 c.153C>T synonymous_variant 0.15 isoniazid
ahpC 2726350 p.Trp53Leu missense_variant 0.28 isoniazid
ahpC 2726358 p.Asp56Lys missense_variant 0.13 isoniazid
ribD 2987323 p.Val162Gly missense_variant 0.18 para-aminosalicylic_acid
Rv2752c 3064632 c.1560C>T synonymous_variant 1.0 rifampicin
isoniazid
thyA 3074595 c.-124C>T upstream_gene_variant 0.17 para-aminosalicylic_acid
thyA 3074601 c.-130T>G upstream_gene_variant 0.21 para-aminosalicylic_acid
thyA 3074608 c.-137A>G upstream_gene_variant 0.2 para-aminosalicylic_acid
thyA 3074641 c.-170C>T upstream_gene_variant 0.19 para-aminosalicylic_acid
thyA 3074645 c.-174T>G upstream_gene_variant 0.28 para-aminosalicylic_acid
thyA 3074648 c.-177T>G upstream_gene_variant 0.25 para-aminosalicylic_acid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339273 c.156T>G synonymous_variant 0.18 delamanid
fbiD 3339279 c.162T>G synonymous_variant 0.11 delamanid
fbiD 3339593 p.His159Pro missense_variant 0.12 delamanid
Rv3083 3448714 p.Asp71His missense_variant 1.0 ethionamide Uncertain significance
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3474597 c.591C>A synonymous_variant 1.0 capreomycin
amikacin
fprA 3475159 p.Asn385Asp missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
fbiB 3642751 p.Asp406Ala missense_variant 0.16 delamanid
clpC1 4038186 p.Ala840Gly missense_variant 0.14 pyrazinamide
clpC1 4039404 p.Glu434Gly missense_variant 0.12 pyrazinamide
clpC1 4040517 p.Val63Ala missense_variant 1.0 pyrazinamide Uncertain significance
embC 4239973 c.111T>G synonymous_variant 0.13 ethambutol
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 1.0 ethambutol Uncertain significance
embC 4242220 c.2358A>C synonymous_variant 0.14 ethambutol
embC 4242393 p.Asp844Ala missense_variant 0.12 ethambutol
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4243848 p.Val206Met missense_variant 1.0 ethambutol Uncertain significance
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Uncertain significance
embB 4249291 c.2778C>A synonymous_variant 0.14 ethambutol
embB 4249293 p.Lys927Arg missense_variant 0.12 ethambutol Uncertain significance
embB 4249298 p.Trp929Gly missense_variant 0.15 ethambutol
embB 4249305 p.Asn931Thr missense_variant 0.23 ethambutol
embB 4249314 p.Phe934Ser missense_variant 0.15 ethambutol
embB 4249323 p.Ala937Glu missense_variant 0.31 ethambutol
aftB 4268776 p.Ser21Gly missense_variant 0.17 capreomycin
amikacin Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Uncertain significance
aftB 4269504 c.-668A>G upstream_gene_variant 0.13 capreomycin
amikacin
ubiA 4269602 p.Val78Ile missense_variant 1.0 ethambutol Uncertain significance
aftB 4269606 c.-770T>C upstream_gene_variant 1.0 capreomycin
amikacin
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338603 c.-82C>T 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 4407873 c.330G>T synonymous_variant 1.0 streptomycin
gid 4407994 p.Ser70Asn missense_variant 0.99 streptomycin Uncertain significance