TB-Profiler result

Run: ERR12544072
Summary

Run ID: ERR12544072

Sample name:

Date: 2024-04-16T04:18:09.514108

Number of reads: 2670602

Percentage reads mapped: 99.55

Median coverage: 74.0

Strain: lineage4.1.2.1;lineage6.2.3

Spoligotype:

Drug-resistance: Sensitive

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage6.2 West-Africa 2 RD702 0.49
lineage4.1 Euro-American None 0.45
lineage4.1.2 Euro-American None 0.46
lineage4.1.2.1 Euro-American (Haarlem) RD182 0.45
lineage4 Euro-American None 0.47
lineage6.2.3 West-Africa 2 RD702 0.52
lineage6 West-Africa 2 RD702 0.54
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
streptomycin
fluoroquinolones
moxifloxacin
ofloxacin
levofloxacin
ciprofloxacin
aminoglycosides
amikacin
capreomycin
kanamycin
cycloserine
ethionamide
clofazimine
para-aminosalicylic_acid
delamanid
bedaquiline
linezolid
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
dnaA 490 p.Gly164Ser missense_variant 0.4 isoniazid Uncertain significance
gyrB 5072 c.-168G>T upstream_gene_variant 0.65 levofloxacin
moxifloxacin
gyrB 6153 p.Ala305Val missense_variant 0.72 levofloxacin
moxifloxacin
gyrB 6446 p.Ala403Ser missense_variant 0.59 levofloxacin Not assoc w R
moxifloxacin Uncertain significance
gyrB 7121 p.Pro628Ser missense_variant 0.69 levofloxacin
moxifloxacin
gyrA 7362 p.Glu21Gln missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7585 p.Ser95Thr missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 7965 p.Arg222Trp missense_variant 0.38 levofloxacin Uncertain significance
moxifloxacin
gyrA 8493 p.Leu398Phe missense_variant 0.65 levofloxacin Uncertain significance
moxifloxacin Uncertain significance
gyrA 9143 c.1842T>C synonymous_variant 0.46 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
gyrA 9304 p.Gly668Asp missense_variant 1.0 levofloxacin Not assoc w R
moxifloxacin Not assoc w R
Rv0010c 13482 p.Ala26Val missense_variant 0.5 isoniazid Not assoc w R
fgd1 491591 p.Lys270Met missense_variant 0.46 clofazimine Not assoc w R
pretomanid
delamanid Uncertain significance
fgd1 491668 p.Lys296Glu missense_variant 0.53 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.57 clofazimine Not assoc w R
pretomanid
delamanid Not assoc w R - Interim
mshA 575679 p.Asn111Ser missense_variant 0.41 ethionamide Not assoc w R
isoniazid Not assoc w R
mshA 575759 p.Arg138Cys missense_variant 0.54 ethionamide
isoniazid
Rv0565c 656298 c.1173G>C synonymous_variant 0.53 ethionamide
Rv0565c 656432 p.Gly347Ser missense_variant 0.57 ethionamide Uncertain significance
Rv0565c 657578 c.-108T>C upstream_gene_variant 0.53 ethionamide
rpoB 759989 c.183G>A synonymous_variant 0.58 rifampicin Not assoc w R - Interim
rpoB 760115 c.309C>T synonymous_variant 0.3 rifampicin Not assoc w R
rpoB 760969 p.Ser388Leu missense_variant 0.7 rifampicin Not assoc w R
rpoB 761723 p.Glu639Asp missense_variant 0.61 rifampicin Not assoc w R
rpoB 763031 c.3225T>C synonymous_variant 0.5 rifampicin Not assoc w R
rpoC 765150 p.Gly594Glu missense_variant 0.47 rifampicin Not assoc w R
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
mmpL5 776100 p.Thr794Ile missense_variant 0.53 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Not assoc w R
Rv1129c 1254551 c.-17T>G upstream_gene_variant 0.53 moxifloxacin Uncertain significance
levofloxacin Uncertain significance
rifampicin Uncertain significance
isoniazid Uncertain significance
Rv1129c 1254562 c.-28T>C upstream_gene_variant 0.52 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
Rv1129c 1254582 c.-48A>C upstream_gene_variant 0.52 moxifloxacin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
fbiC 1302899 c.-32A>G upstream_gene_variant 0.6 clofazimine Uncertain significance
pretomanid
delamanid Uncertain significance
Rv1258c 1406685 p.Val219Ala missense_variant 0.64 streptomycin Uncertain significance
isoniazid Uncertain significance
pyrazinamide Uncertain significance
embR 1417554 c.-207C>G upstream_gene_variant 0.58 ethambutol
atpE 1461251 c.207G>T synonymous_variant 0.64 bedaquiline Not assoc w R - Interim
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 streptomycin
kanamycin
capreomycin
amikacin
inhA 1674434 p.Val78Ala missense_variant 0.6 ethionamide Uncertain significance
isoniazid Not assoc w R
tsnR 1854300 p.Leu232Pro missense_variant 1.0 linezolid Not assoc w R
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin Not assoc w R
bacA 2062922 p.Ile603Val missense_variant 0.39 streptomycin Not assoc w R
kanamycin Not assoc w R
capreomycin Not assoc w R
amikacin Not assoc w R
bacA 2063121 c.1608A>T synonymous_variant 0.61 streptomycin Not assoc w R - Interim
kanamycin Not assoc w R - Interim
capreomycin Not assoc w R - Interim
amikacin Not assoc w R - Interim
katG 2154724 p.Arg463Leu missense_variant 0.5 isoniazid Not assoc w R
katG 2155503 c.609C>T synonymous_variant 0.61 isoniazid Not assoc w R
PPE35 2167926 p.Leu896Ser missense_variant 0.66 pyrazinamide Not assoc w R
PPE35 2169269 c.1340_1344delGCCAAinsT frameshift_variant&missense_variant 0.6 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.68 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Not assoc w R
bedaquiline Not assoc w R - Interim
kasA 2518076 c.-39C>T upstream_gene_variant 0.34 isoniazid
kasA 2518132 c.18C>T synonymous_variant 0.72 isoniazid
Rv2477c 2783007 p.Arg346Cys missense_variant 0.64 ethambutol Uncertain significance
moxifloxacin Uncertain significance
streptomycin Uncertain significance
levofloxacin Uncertain significance
kanamycin Uncertain significance
rifampicin Uncertain significance
amikacin Uncertain significance
ribD 2987354 c.516G>A synonymous_variant 0.52 para-aminosalicylic_acid
Rv2680 2996085 c.-20G>A upstream_gene_variant 0.59 capreomycin Uncertain significance
Rv2680 2996136 p.Ser11Asn missense_variant 0.17 capreomycin
Rv2752c 3064905 c.1287C>T synonymous_variant 0.86 ethambutol Not assoc w R - Interim
moxifloxacin
levofloxacin
rifampicin Not assoc w R - Interim
isoniazid Not assoc w R - Interim
ald 3086728 c.-92C>T upstream_gene_variant 0.6 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 1.0 cycloserine
ald 3087084 c.266delA frameshift_variant 0.45 cycloserine
Rv3236c 3612800 p.Val106Ala missense_variant 0.64 pyrazinamide Uncertain significance
lpqB 3624350 c.561G>T synonymous_variant 0.63 bedaquiline Not assoc w R - Interim
rifampicin Not assoc w R
lpqB 3624486 p.Asp142Gly missense_variant 0.6 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrB 3625065 p.Met517Leu missense_variant 1.0 bedaquiline Uncertain significance
rifampicin Not assoc w R
mtrA 3627756 c.-407A>T upstream_gene_variant 0.43 bedaquiline
rifampicin
alr 3840559 p.Arg288Ser missense_variant 0.56 cycloserine
alr 3840618 p.Asp268Gly missense_variant 0.56 cycloserine
glpK 4138377 p.Val460Ala missense_variant 0.64 ethambutol Not assoc w R
moxifloxacin Not assoc w R
streptomycin Not assoc w R
levofloxacin Not assoc w R
rifampicin Not assoc w R
isoniazid Not assoc w R
embC 4239298 c.-565C>T upstream_gene_variant 0.52 ethambutol Not assoc w R
embC 4240671 p.Thr270Ile missense_variant 0.43 ethambutol Not assoc w R
embC 4241843 p.Leu661Ile missense_variant 0.56 ethambutol Not assoc w R
embC 4242643 c.2781C>T synonymous_variant 1.0 ethambutol Not assoc w R
embC 4242803 p.Val981Leu missense_variant 0.49 ethambutol Not assoc w R
embC 4242910 p.Phe1016Leu missense_variant 0.45 ethambutol
embA 4243541 c.309C>T synonymous_variant 0.56 ethambutol Not assoc w R - Interim
embA 4244220 c.988C>T synonymous_variant 0.54 ethambutol Not assoc w R
embA 4244379 p.Pro383Ser missense_variant 0.55 ethambutol Not assoc w R
embB 4246864 c.351C>T synonymous_variant 0.44 ethambutol Not assoc w R
embB 4247646 p.Glu378Ala missense_variant 0.45 ethambutol Not assoc w R
aftB 4268052 p.Arg262Gln missense_variant 0.57 ethambutol
ubiA 4269351 c.483C>T synonymous_variant 0.49 ethambutol Not assoc w R
ubiA 4269387 p.Glu149Asp missense_variant 0.56 ethambutol Not assoc w R
ubiA 4269522 c.312C>T synonymous_variant 0.55 ethambutol Not assoc w R
ubiA 4269606 c.228T>C synonymous_variant 0.48 ethambutol Not assoc w R
ethA 4326465 p.Ile337Val missense_variant 0.52 ethionamide Uncertain significance
ethR 4328030 p.Ala161Gly missense_variant 0.3 ethionamide
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 capreomycin Not assoc w R
amikacin Not assoc w R
kanamycin Not assoc w R
whiB6 4338732 c.-211C>T upstream_gene_variant 1.0 capreomycin
amikacin
kanamycin
gid 4407588 c.615A>G synonymous_variant 0.57 streptomycin Not assoc w R