TB-Profiler result

Run: 7233e289-15bf-4c4c-bfe8-b0d4488b7377
Summary

Run ID: 7233e289-15bf-4c4c-bfe8-b0d4488b7377

Sample name:

Date: 07-05-2024 10:09:12

Number of reads: 4372741

Percentage reads mapped: 97.71

Median coverage: 99

Strain: lineage6.3.1;lineage4.1.3

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 0.18
lineage6 West-Africa 2 RD702 0.78
lineage4.1 Euro-American None 0.17
lineage6.3 West-Africa 2 RD702 0.77
lineage4.1.3 Euro-American None 0.14
lineage6.3.1 West-Africa 2 RD702 0.79
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 inhA c.-154G>A Assoc w R
katG p.Ser315Thr Assoc w R
ethambutol embB p.Met306Ile Assoc w R
pyrazinamide
moxifloxacin
levofloxacin
bedaquiline
delamanid
pretomanid
linezolid
streptomycin gid p.Leu79Ser Uncertain significance
amikacin
kanamycin
capreomycin
clofazimine
ethionamide inhA c.-154G>A Assoc w R - interim
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 0.18 rifampicin Assoc w R
inhA 1674048 c.-154G>A upstream_gene_variant 0.21 isoniazid Assoc w R
ethionamide Assoc w R - interim
katG 2155168 p.Ser315Thr missense_variant 0.16 isoniazid Assoc w R
embB 4247431 p.Met306Ile missense_variant 0.19 ethambutol Assoc w R
gid 4407967 p.Leu79Ser missense_variant 0.28 streptomycin 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
gyrB 6446 p.Ala403Ser missense_variant 0.82 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 6922 c.-380G>T upstream_gene_variant 0.19 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6932 p.Gln565Lys missense_variant 0.11 fluoroquinolones
moxifloxacin
levofloxacin
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 0.8 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
gyrA 9557 c.2256G>C synonymous_variant 0.21 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9591 p.Gly764Arg missense_variant 0.76 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 490751 c.-32T>G upstream_gene_variant 0.16 delamanid
fgd1 490759 c.-24A>T upstream_gene_variant 0.17 delamanid
fgd1 490771 c.-12T>G upstream_gene_variant 0.13 delamanid
fgd1 491014 p.Thr78Pro missense_variant 0.14 delamanid
fgd1 491668 p.Lys296Glu missense_variant 0.84 delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.87 delamanid
mshA 576741 p.Ala465Gly missense_variant 0.12 ethionamide
isoniazid
mshA 576744 p.Val466Gly missense_variant 0.18 ethionamide
isoniazid
ccsA 620551 p.Asp221His missense_variant 0.23 capreomycin
amikacin
ccsA 620561 p.Thr224Asn missense_variant 0.11 capreomycin
amikacin
ccsA 620567 p.Asp226Gly missense_variant 0.17 capreomycin
amikacin
ccsA 620756 p.Asp289Gly missense_variant 0.13 capreomycin
amikacin
ccsA 620773 p.Ile295Val missense_variant 0.17 capreomycin
amikacin
rpoB 759615 c.-192A>C upstream_gene_variant 0.31 rifampicin
rpoB 759620 c.-187A>C upstream_gene_variant 0.26 rifampicin
rpoB 760969 p.Ser388Leu missense_variant 0.79 rifampicin Uncertain significance
rpoB 761723 p.Glu639Asp missense_variant 0.78 rifampicin Uncertain significance
rpoC 763031 c.-339T>C upstream_gene_variant 0.83 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.24 rifampicin Uncertain significance
mmpL5 775639 p.Ile948Val missense_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
mmpL5 776100 p.Thr794Ile missense_variant 0.8 clofazimine Uncertain significance
bedaquiline Uncertain significance
rpsL 781395 c.-165T>C upstream_gene_variant 1.0 streptomycin Uncertain significance
rpsL 781421 c.-139C>A upstream_gene_variant 0.25 streptomycin Uncertain significance
fbiC 1302899 c.-32A>G upstream_gene_variant 0.91 delamanid Uncertain significance
fbiC 1303016 p.Val29Gly missense_variant 0.19 delamanid
fbiC 1304159 p.Val410Gly missense_variant 0.25 delamanid
fbiC 1304166 c.1236A>G synonymous_variant 0.19 delamanid
fbiC 1304610 c.1680C>T synonymous_variant 0.14 delamanid
Rv1258c 1407055 p.Tyr96Asp missense_variant 0.19 streptomycin
pyrazinamide
isoniazid
atpE 1461251 c.207G>T synonymous_variant 0.8 bedaquiline
rrs 1471659 n.-187C>T upstream_gene_variant 1.0 linezolid
kanamycin
capreomycin
amikacin
aminoglycosides
streptomycin
rrl 1474489 n.832T>G non_coding_transcript_exon_variant 0.13 linezolid
inhA 1674434 p.Val78Ala missense_variant 0.87 ethionamide Uncertain significance
isoniazid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
ndh 2102694 p.Val117Ile missense_variant 0.81 ethionamide Uncertain significance
isoniazid Uncertain significance
ndh 2103225 c.-183A>C upstream_gene_variant 0.16 ethionamide
isoniazid
ndh 2103235 c.-193C>G upstream_gene_variant 0.13 ethionamide
isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.84 isoniazid Uncertain significance
katG 2155503 c.609C>T synonymous_variant 0.76 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.86 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.86 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222852 p.Ala105Thr missense_variant 0.83 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
pncA 2288841 p.Ala134Gly missense_variant 0.19 pyrazinamide Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.87 isoniazid
eis 2714561 p.Gly258Cys missense_variant 0.14 kanamycin
amikacin
ahpC 2726338 p.Val49Gly missense_variant 0.28 isoniazid
ahpC 2726341 p.Val50Gly missense_variant 0.28 isoniazid
ahpC 2726345 c.153C>T synonymous_variant 0.18 isoniazid
ahpC 2726350 p.Trp53Leu missense_variant 0.28 isoniazid
ahpC 2726358 p.Asp56Asn missense_variant 0.16 isoniazid
ribD 2987323 p.Val162Gly missense_variant 0.2 para-aminosalicylic_acid
thyA 3074641 c.-170C>T upstream_gene_variant 0.14 para-aminosalicylic_acid
thyA 3074645 c.-174T>G upstream_gene_variant 0.16 para-aminosalicylic_acid
thyA 3074648 c.-177T>G upstream_gene_variant 0.21 para-aminosalicylic_acid
ald 3086728 c.-92C>T upstream_gene_variant 0.86 cycloserine
ald 3086788 c.-32T>C upstream_gene_variant 0.99 cycloserine
ald 3087084 c.266delA frameshift_variant 0.83 cycloserine
Rv3083 3449781 c.1278G>A synonymous_variant 0.83 ethionamide
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3475159 p.Asn385Asp missense_variant 0.77 capreomycin Uncertain significance
amikacin Uncertain significance
whiB7 3568419 c.261C>A synonymous_variant 0.12 streptomycin
kanamycin
amikacin
fbiB 3642397 p.Ala288Val missense_variant 0.81 delamanid
rpoA 3877696 p.Thr271Ile missense_variant 0.83 rifampicin Uncertain significance
rpoA 3878613 c.-113_-107delCAACCCA upstream_gene_variant 0.41 rifampicin
clpC1 4039484 c.1221T>G synonymous_variant 0.16 pyrazinamide
embC 4240671 p.Thr270Ile missense_variant 0.85 ethambutol Uncertain significance
embC 4241843 p.Leu661Ile missense_variant 0.85 ethambutol Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embC 4242803 p.Val981Leu missense_variant 0.23 ethambutol Uncertain significance
embA 4243217 c.-16C>A upstream_gene_variant 0.12 ethambutol Uncertain significance
embA 4244220 c.988C>T synonymous_variant 0.77 ethambutol
embA 4244379 p.Pro383Ser missense_variant 0.8 ethambutol Uncertain significance
embB 4246864 c.351C>T synonymous_variant 0.75 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.84 ethambutol Uncertain significance
embB 4248478 c.1965G>A synonymous_variant 0.79 ethambutol
embB 4249298 p.Trp929Gly missense_variant 0.12 ethambutol
embB 4249323 p.Ala937Glu missense_variant 0.25 ethambutol
aftB 4268477 c.360C>T synonymous_variant 0.77 capreomycin
amikacin
aftB 4269351 c.-515C>T upstream_gene_variant 0.81 capreomycin
amikacin
ubiA 4269387 p.Glu149Asp missense_variant 0.84 ethambutol Uncertain significance
ubiA 4269502 p.Val111Gly missense_variant 0.14 ethambutol Uncertain significance
aftB 4269504 c.-668A>G upstream_gene_variant 0.18 capreomycin
amikacin
aftB 4269522 c.-686C>T upstream_gene_variant 0.76 capreomycin
amikacin
aftB 4269606 c.-770T>C upstream_gene_variant 0.8 capreomycin
amikacin
ethA 4326465 p.Ile337Val missense_variant 0.8 ethionamide Uncertain significance
whiB6 4338478 p.Phe15Ser missense_variant 0.84 streptomycin
capreomycin
amikacin
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
whiB6 4338661 c.-140C>T upstream_gene_variant 0.19 streptomycin
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.86 streptomycin