TB-Profiler result

Run: dee7d280-05dc-4f05-8a91-095bc9ca58db
Summary

Run ID: dee7d280-05dc-4f05-8a91-095bc9ca58db

Sample name:

Date: 15-05-2024 06:08:33

Number of reads: 2966578

Percentage reads mapped: 95.69

Median coverage: 160

Strain: lineage1.2.1.2.1

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
lineage1 Indo-Oceanic RD239 1.0
lineage1.2.1 Indo-Oceanic RD239 1.0
lineage1.2.1.2 Indo-Oceanic RD239 1.0
lineage1.2.1.2.1 Indo-Oceanic RD239 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
ethambutol embB p.Met306Leu Assoc w R
p.Asp1024Asn Uncertain significance
pyrazinamide pncA p.Cys72Arg Assoc w R - interim
moxifloxacin gyrA p.Asp94Asn Assoc w R
levofloxacin gyrA p.Asp94Asn Assoc w R
bedaquiline
delamanid
pretomanid
linezolid
streptomycin
amikacin
kanamycin
capreomycin
clofazimine
ethionamide
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 7581 p.Asp94Asn missense_variant 0.15 ofloxacin Uncertain significance
moxifloxacin Assoc w R
levofloxacin Assoc w R
fluoroquinolones Uncertain significance
ciprofloxacin Uncertain significance
rpoB 761155 p.Ser450Leu missense_variant 0.99 rifampicin Assoc w R
pncA 2289028 p.Cys72Arg missense_variant 1.0 pyrazinamide Assoc w R - interim
embB 4247429 p.Met306Leu missense_variant 1.0 ethambutol Assoc w R
embB 4249583 p.Asp1024Asn missense_variant 1.0 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 6112 p.Met291Ile missense_variant 0.99 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
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 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9143 c.1842T>C synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9260 c.1959G>C synonymous_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
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 575368 c.21T>C synonymous_variant 1.0 ethionamide
isoniazid
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
rpoC 763531 c.162G>C synonymous_variant 1.0 rifampicin
rpoC 763884 p.Ala172Val missense_variant 1.0 rifampicin Uncertain significance
rpoC 763886 c.517C>A synonymous_variant 1.0 rifampicin
rpoC 764809 c.1440C>T synonymous_variant 1.0 rifampicin
rpoC 764944 p.His525Gln 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
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
fbiC 1302821 c.-110G>A upstream_gene_variant 1.0 delamanid Uncertain significance
Rv1258c 1406312 c.1029T>C synonymous_variant 1.0 streptomycin
pyrazinamide
isoniazid
embR 1417019 p.Cys110Tyr missense_variant 1.0 ethambutol Uncertain significance
atpE 1460907 c.-138T>C upstream_gene_variant 1.0 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
inhA 1673406 c.-796C>T upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674162 c.-40C>T upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
inhA 1674272 p.His24Pro missense_variant 0.99 ethionamide
isoniazid
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
tlyA 1918189 p.Arg84Gly missense_variant 1.0 capreomycin
ndh 2102198 c.844_845insT frameshift_variant 1.0 ethionamide
isoniazid
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
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 2519048 p.Gly312Ser missense_variant 0.99 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339417 c.300A>G synonymous_variant 1.0 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
fprA 3475296 c.1290G>A synonymous_variant 1.0 capreomycin
amikacin
whiB7 3568488 c.191delG frameshift_variant 1.0 streptomycin Uncertain significance
kanamycin Uncertain significance
amikacin Uncertain significance
fbiB 3640557 c.-978T>C upstream_gene_variant 1.0 delamanid
clpC1 4040517 p.Val63Ala missense_variant 1.0 pyrazinamide Uncertain significance
embC 4240671 p.Thr270Ile missense_variant 1.0 ethambutol Uncertain significance
embC 4241042 p.Asn394Asp missense_variant 1.0 ethambutol Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embA 4243580 c.348G>A synonymous_variant 1.0 ethambutol
embA 4244420 c.1188G>C synonymous_variant 1.0 ethambutol
embA 4245969 p.Pro913Ser missense_variant 1.0 ethambutol Uncertain significance
embB 4247578 c.1065G>A synonymous_variant 1.0 ethambutol
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Uncertain significance
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Uncertain significance
aftB 4269606 c.-770T>C upstream_gene_variant 1.0 capreomycin
amikacin
ubiA 4269864 c.-32delG upstream_gene_variant 1.0 ethambutol
whiB6 4338361 p.Arg54Gln missense_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
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