TB-Profiler result

Run: 40568e6a-4629-4d9b-aa80-914aa95fb3af
Summary

Run ID: 40568e6a-4629-4d9b-aa80-914aa95fb3af

Sample name:

Date: 28-03-2023 13:54:02

Number of reads: 3672994

Percentage reads mapped: 96.74

Median coverage: 94

Strain: lineage1.2.1.2.1

Spoligotype:

Drug-resistance: Sensitive

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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
isoniazid
ethambutol
pyrazinamide
moxifloxacin
levofloxacin
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
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 6428 p.Glu397Lys missense_variant 1.0 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 7362 p.Glu21Gln missense_variant 0.99 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 490756 c.-27T>G upstream_gene_variant 0.16 delamanid
fgd1 491742 c.960T>C synonymous_variant 1.0 delamanid
mshA 575368 c.21T>C synonymous_variant 1.0 ethionamide
isoniazid
mshA 576106 c.759C>G synonymous_variant 0.15 ethionamide
isoniazid
mshA 576108 p.Ala254Gly missense_variant 0.3 ethionamide Uncertain significance
isoniazid
mshA 576456 p.Val370Gly missense_variant 0.29 ethionamide
isoniazid
mshA 576483 p.Val379Gly missense_variant 0.22 ethionamide
isoniazid
mshA 576613 c.1266A>C synonymous_variant 0.28 ethionamide
isoniazid
rpoB 761161 p.Leu452Arg missense_variant 0.17 rifampicin
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 0.99 rifampicin
rpoC 764367 p.Gly333Ala missense_variant 0.16 rifampicin
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
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
rrl 1474639 n.982G>A non_coding_transcript_exon_variant 1.0 linezolid Uncertain significance
rrl 1474936 n.1279C>A non_coding_transcript_exon_variant 0.17 linezolid
rrl 1475194 n.1537C>T non_coding_transcript_exon_variant 0.12 linezolid Uncertain significance
rrl 1476058 n.2401T>G non_coding_transcript_exon_variant 0.3 linezolid
fabG1 1673553 p.Asp38Glu missense_variant 0.23 ethionamide
isoniazid
inhA 1674162 c.-40C>T upstream_gene_variant 1.0 ethionamide Uncertain significance
isoniazid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
katG 2154724 p.Arg463Leu missense_variant 1.0 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 1.0 pyrazinamide Uncertain significance
PPE35 2170035 p.Val193Gly missense_variant 0.25 pyrazinamide
PPE35 2170059 p.Val185Gly missense_variant 0.25 pyrazinamide
PPE35 2170065 p.Ala183Gly missense_variant 0.36 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 2519048 p.Gly312Ser missense_variant 1.0 isoniazid
kasA 2519071 p.Asp319Glu missense_variant 0.2 isoniazid
ahpC 2726051 c.-142G>A upstream_gene_variant 1.0 isoniazid
pepQ 2859931 p.Leu163Arg missense_variant 0.23 clofazimine
bedaquiline
pepQ 2860159 p.Ala87Gly missense_variant 0.22 clofazimine
bedaquiline
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339417 c.300A>G synonymous_variant 1.0 delamanid
fbiD 3339705 c.588G>A synonymous_variant 1.0 delamanid
fbiD 3339751 p.Ala212Pro missense_variant 0.24 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
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
rpoA 3878567 c.-60C>G upstream_gene_variant 0.15 rifampicin
rpoA 3878578 c.-71C>A upstream_gene_variant 0.2 rifampicin
rpoA 3878580 c.-73A>C upstream_gene_variant 0.15 rifampicin
rpoA 3878590 c.-83G>C upstream_gene_variant 0.27 rifampicin
rpoA 3878641 c.-134C>G upstream_gene_variant 0.62 rifampicin
clpC1 4040517 p.Val63Ala missense_variant 1.0 pyrazinamide Uncertain significance
embC 4240409 p.Pro183Ala missense_variant 0.27 ethambutol
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 4246527 p.Ala5Gly missense_variant 0.19 ethambutol
embB 4246544 p.Thr11Pro missense_variant 0.14 ethambutol Uncertain significance
embB 4247578 c.1065G>A synonymous_variant 1.0 ethambutol
embB 4247646 p.Glu378Ala missense_variant 1.0 ethambutol Uncertain significance
aftB 4268619 p.Val73Gly missense_variant 0.22 capreomycin
amikacin
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
ethA 4328415 c.-942A>G upstream_gene_variant 0.22 ethionamide
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 0.99 streptomycin