TB-Profiler result

Run: 37d5c7da-a228-496c-8b89-592cab7830a5
Summary

Run ID: 37d5c7da-a228-496c-8b89-592cab7830a5

Sample name:

Date: 04-12-2023 05:02:16

Number of reads: 372884

Percentage reads mapped: 94.98

Median coverage: 8

Strain: lineage6.3.1;lineage4.6

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 0.12
lineage6 West-Africa 2 RD702 0.89
lineage4.6 Euro-American None 0.09
lineage6.3 West-Africa 2 RD702 0.92
lineage6.3.1 West-Africa 2 RD702 0.89
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
gyrA 9143 c.1842T>C synonymous_variant 0.67 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
rpoB 760969 p.Ser388Leu missense_variant 0.73 rifampicin Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 0.83 clofazimine Uncertain significance
bedaquiline 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
PPE35 2167926 p.Leu896Ser missense_variant 0.82 pyrazinamide Uncertain significance
PPE35 2168731 p.Pro628Thr missense_variant 1.0 pyrazinamide
Rv1979c 2222852 p.Ala105Thr missense_variant 0.93 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2288879 c.363G>A synonymous_variant 1.0 pyrazinamide
kasA 2518132 c.18C>T synonymous_variant 1.0 isoniazid
ald 3086728 c.-92C>T upstream_gene_variant 0.91 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.93 cycloserine
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3475159 p.Asn385Asp missense_variant 1.0 capreomycin Uncertain significance
amikacin Uncertain significance
rpoA 3877696 p.Thr271Ile missense_variant 1.0 rifampicin Uncertain significance
embC 4241843 p.Leu661Ile missense_variant 1.0 ethambutol Uncertain significance
embB 4247646 p.Glu378Ala missense_variant 0.9 ethambutol Uncertain significance
aftB 4268477 c.360C>T synonymous_variant 0.87 capreomycin
amikacin
aftB 4269351 c.-515C>T upstream_gene_variant 0.9 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 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance