TB-Profiler result

Run: dbc5245b-bd47-4c84-ac71-adc5b6c55adf
Summary

Run ID: dbc5245b-bd47-4c84-ac71-adc5b6c55adf

Sample name:

Date: 04-12-2023 05:00:53

Number of reads: 383671

Percentage reads mapped: 95.31

Median coverage: 8

Strain: lineage6.3.1;lineage4

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.1
lineage6 West-Africa 2 RD702 0.9
lineage6.3 West-Africa 2 RD702 0.89
lineage6.3.1 West-Africa 2 RD702 0.88
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 6446 p.Ala403Ser missense_variant 0.85 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 9143 c.1842T>C synonymous_variant 0.9 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 0.9 delamanid
rpoB 760671 c.865C>T synonymous_variant 1.0 rifampicin
rpoB 760969 p.Ser388Leu missense_variant 0.8 rifampicin Uncertain significance
rpoC 763031 c.-339T>C upstream_gene_variant 1.0 rifampicin
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 1302899 c.-32A>G upstream_gene_variant 0.9 delamanid Uncertain significance
atpE 1461251 c.207G>T synonymous_variant 0.93 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
inhA 1674434 p.Val78Ala missense_variant 0.7 ethionamide Uncertain significance
isoniazid Uncertain significance
katG 2154724 p.Arg463Leu missense_variant 0.9 isoniazid Uncertain significance
PPE35 2167926 p.Leu896Ser missense_variant 0.85 pyrazinamide Uncertain significance
PPE35 2168731 p.Pro628Thr missense_variant 0.9 pyrazinamide
Rv1979c 2222308 p.Asp286Gly missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222852 p.Ala105Thr missense_variant 0.92 clofazimine Uncertain significance
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.91 isoniazid
ald 3086728 c.-92C>T upstream_gene_variant 0.82 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 1.0 cycloserine
Rv3083 3449781 c.1278G>A synonymous_variant 0.8 ethionamide
embA 4244220 c.988C>T synonymous_variant 0.91 ethambutol
aftB 4269351 c.-515C>T upstream_gene_variant 0.94 capreomycin
amikacin
ubiA 4269387 p.Glu149Asp missense_variant 1.0 ethambutol Uncertain significance
ethA 4326465 p.Ile337Val missense_variant 1.0 ethionamide Uncertain significance
whiB6 4338176 p.Ala116Thr missense_variant 0.3 streptomycin
capreomycin
amikacin