TB-Profiler result

Run: d051c057-1ac5-4437-9dd3-8b46756ad976
Summary

Run ID: d051c057-1ac5-4437-9dd3-8b46756ad976

Sample name:

Date: 17-02-2023 12:18:45

Number of reads: 1886737

Percentage reads mapped: 99.09

Median coverage: 61

Strain: lineage4.1.1.3

Spoligotype:

Drug-resistance: MDR-TB

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 1.0
lineage4.1 Euro-American None 1.0
lineage4.1.1 Euro-American (X-type) None 1.0
lineage4.1.1.3 Euro-American (X-type) RD193 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.Leu452Pro Assoc w R
isoniazid katG p.Ser315Thr Assoc w R
ahpC p.Asp73His Uncertain significance
ethambutol
pyrazinamide pncA p.Trp68* Assoc w R - interim
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
rpoB 761161 p.Leu452Pro missense_variant 1.0 rifampicin Assoc w R
katG 2155168 p.Ser315Thr missense_variant 1.0 isoniazid Assoc w R
pncA 2289039 p.Trp68* stop_gained 1.0 pyrazinamide Assoc w R - interim
ahpC 2726409 p.Asp73His missense_variant 1.0 isoniazid 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
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 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
mshA 576108 p.Ala254Gly missense_variant 0.31 ethionamide Uncertain significance
isoniazid
mshA 576482 p.Val379Leu missense_variant 0.21 ethionamide
isoniazid
rpoC 764584 c.1215G>A synonymous_variant 1.0 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 1.0 rifampicin Uncertain significance
rpoC 765454 c.2085C>A synonymous_variant 1.0 rifampicin
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 0.98 streptomycin Uncertain significance
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
katG 2154678 c.1434G>C synonymous_variant 1.0 isoniazid
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
fbiD 3339734 p.Ala206Gly missense_variant 0.4 delamanid
Rv3083 3449670 c.1167C>A synonymous_variant 1.0 ethionamide
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
alr 3840911 c.510A>G synonymous_variant 1.0 cycloserine
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embC 4242803 p.Val981Leu missense_variant 1.0 ethambutol Uncertain significance
embB 4246567 c.54_55insT frameshift_variant 0.18 ethambutol
embB 4246584 p.Arg24Pro missense_variant 0.23 ethambutol
embB 4249408 c.2895G>A synonymous_variant 1.0 ethambutol
embB 4249678 c.3165C>A synonymous_variant 1.0 ethambutol
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407785 p.Ala140Pro missense_variant 1.0 streptomycin