TB-Profiler result

Run: d7a1987b-1f4f-4fbd-894a-1ea8f03c63b7
Summary

Run ID: d7a1987b-1f4f-4fbd-894a-1ea8f03c63b7

Sample name:

Date: 08-05-2024 17:20:24

Number of reads: 4691359

Percentage reads mapped: 97.8

Median coverage: 107

Strain: lineage6.3.1;lineage4.1.3

Spoligotype:

Drug-resistance: Other

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Lineage Table: The lineage is inferred by analysing lineage specific SNPs
Lineage Family RDs Frequency
lineage4 Euro-American None 0.16
lineage6 West-Africa 2 RD702 0.83
lineage4.1 Euro-American None 0.18
lineage6.3 West-Africa 2 RD702 0.82
lineage4.1.3 Euro-American None 0.17
lineage6.3.1 West-Africa 2 RD702 0.83
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 gid c.351delG Assoc w R - interim
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
gid 4407851 c.351delG frameshift_variant 0.18 streptomycin Assoc w R - interim
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 5914 p.Asp225Glu missense_variant 0.16 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrB 6446 p.Ala403Ser missense_variant 0.88 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 0.79 fluoroquinolones
moxifloxacin
levofloxacin
ciprofloxacin
ofloxacin
gyrA 9304 p.Gly668Asp missense_variant 1.0 fluoroquinolones
moxifloxacin Uncertain significance
levofloxacin Uncertain significance
ciprofloxacin
ofloxacin
fgd1 490751 c.-32T>G upstream_gene_variant 0.17 delamanid
fgd1 490759 c.-24A>T upstream_gene_variant 0.15 delamanid
fgd1 490780 c.-3C>A upstream_gene_variant 0.13 delamanid
fgd1 491014 p.Thr78Pro missense_variant 0.22 delamanid
fgd1 491668 p.Lys296Glu missense_variant 0.85 delamanid Uncertain significance
fgd1 491742 c.960T>C synonymous_variant 0.82 delamanid
mshA 576741 p.Ala465Gly missense_variant 0.17 ethionamide
isoniazid
mshA 576751 p.Lys468Asn missense_variant 0.14 ethionamide
isoniazid
ccsA 619862 c.-29G>A upstream_gene_variant 0.79 capreomycin
amikacin
rpoB 759611 c.-196G>C upstream_gene_variant 0.12 rifampicin
rpoB 759615 c.-192A>C upstream_gene_variant 0.23 rifampicin
rpoB 759620 c.-187A>C upstream_gene_variant 0.27 rifampicin
rpoB 759916 p.Lys37Thr missense_variant 0.14 rifampicin
rpoB 760969 p.Ser388Leu missense_variant 0.86 rifampicin Uncertain significance
rpoB 761723 p.Glu639Asp missense_variant 0.82 rifampicin Uncertain significance
rpoC 763031 c.-339T>C upstream_gene_variant 0.84 rifampicin
rpoC 765150 p.Gly594Glu missense_variant 0.12 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 0.21 streptomycin Uncertain significance
fbiC 1302899 c.-32A>G upstream_gene_variant 0.8 delamanid Uncertain significance
fbiC 1303016 p.Val29Gly missense_variant 0.17 delamanid
fbiC 1304143 p.Trp405Gly missense_variant 0.11 delamanid
fbiC 1304159 p.Val410Gly missense_variant 0.23 delamanid
fbiC 1304166 c.1236A>G synonymous_variant 0.18 delamanid
fbiC 1304174 p.Val415Gly missense_variant 0.11 delamanid
fbiC 1304610 c.1680C>T synonymous_variant 0.15 delamanid
atpE 1461101 c.57T>G synonymous_variant 0.11 bedaquiline
atpE 1461251 c.207G>T synonymous_variant 0.82 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
fabG1 1674076 p.Thr213Pro missense_variant 0.12 ethionamide
isoniazid
inhA 1674434 p.Val78Ala missense_variant 0.82 ethionamide Uncertain significance
isoniazid Uncertain significance
tlyA 1917972 c.33A>G synonymous_variant 1.0 capreomycin
ndh 2102694 p.Val117Ile missense_variant 0.86 ethionamide Uncertain significance
isoniazid Uncertain significance
ndh 2103225 c.-183A>C upstream_gene_variant 0.15 ethionamide
isoniazid
katG 2154724 p.Arg463Leu missense_variant 0.86 isoniazid Uncertain significance
katG 2155503 c.609C>T synonymous_variant 0.8 isoniazid
PPE35 2167926 p.Leu896Ser missense_variant 0.8 pyrazinamide Uncertain significance
Rv1979c 2222308 p.Asp286Gly missense_variant 0.87 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2222852 p.Ala105Thr missense_variant 0.81 clofazimine Uncertain significance
bedaquiline Uncertain significance
Rv1979c 2223293 c.-129A>G upstream_gene_variant 1.0 clofazimine Uncertain significance
bedaquiline Uncertain significance
kasA 2518132 c.18C>T synonymous_variant 0.74 isoniazid
eis 2714539 p.Ile265Asn missense_variant 0.12 kanamycin
amikacin
eis 2714549 p.Met262Leu missense_variant 0.21 kanamycin
amikacin
eis 2714561 p.Gly258Cys missense_variant 0.15 kanamycin
amikacin
eis 2714566 p.Leu256Pro missense_variant 0.19 kanamycin Uncertain significance
amikacin
ahpC 2726093 c.-100T>A upstream_gene_variant 0.79 isoniazid
ahpC 2726338 p.Val49Gly missense_variant 0.31 isoniazid
ahpC 2726341 p.Val50Gly missense_variant 0.32 isoniazid
ahpC 2726345 c.153C>T synonymous_variant 0.21 isoniazid
ahpC 2726350 p.Trp53Leu missense_variant 0.29 isoniazid
ahpC 2726358 p.Asp56Lys missense_variant 0.2 isoniazid
thyA 3074641 c.-170C>T upstream_gene_variant 0.14 para-aminosalicylic_acid
thyA 3074645 c.-174T>G upstream_gene_variant 0.12 para-aminosalicylic_acid
thyA 3074648 c.-177T>G upstream_gene_variant 0.19 para-aminosalicylic_acid
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 0.64 cycloserine
fbiD 3339273 c.156T>G synonymous_variant 0.15 delamanid
Rv3083 3449781 c.1278G>A synonymous_variant 0.8 ethionamide
fprA 3473996 c.-11_-10insA upstream_gene_variant 1.0 capreomycin
amikacin
fprA 3475159 p.Asn385Asp missense_variant 0.82 capreomycin Uncertain significance
amikacin Uncertain significance
rpoA 3877696 p.Thr271Ile missense_variant 0.8 rifampicin Uncertain significance
rpoA 3878576 c.-69T>C upstream_gene_variant 0.12 rifampicin
rpoA 3878580 c.-73A>C upstream_gene_variant 0.13 rifampicin
rpoA 3878590 c.-83G>C upstream_gene_variant 0.11 rifampicin
clpC1 4039484 c.1221T>G synonymous_variant 0.13 pyrazinamide
embC 4240648 c.786C>T synonymous_variant 0.13 ethambutol
embC 4240671 p.Thr270Ile missense_variant 0.73 ethambutol Uncertain significance
embC 4241843 p.Leu661Ile missense_variant 0.82 ethambutol Uncertain significance
embA 4242643 c.-590C>T upstream_gene_variant 1.0 ethambutol
embC 4242803 p.Val981Leu missense_variant 0.17 ethambutol Uncertain significance
embA 4243969 p.Val246Ala missense_variant 0.19 ethambutol
embA 4244220 c.988C>T synonymous_variant 0.79 ethambutol
embA 4244379 p.Pro383Ser missense_variant 0.79 ethambutol Uncertain significance
embB 4246864 c.351C>T synonymous_variant 0.84 ethambutol
embB 4247646 p.Glu378Ala missense_variant 0.79 ethambutol Uncertain significance
embB 4249298 p.Trp929Gly missense_variant 0.11 ethambutol
embB 4249305 p.Asn931Thr missense_variant 0.15 ethambutol
embB 4249323 p.Ala937Glu missense_variant 0.26 ethambutol
aftB 4268477 c.360C>T synonymous_variant 0.84 capreomycin
amikacin
aftB 4269351 c.-515C>T upstream_gene_variant 0.82 capreomycin
amikacin
ubiA 4269387 p.Glu149Asp missense_variant 0.78 ethambutol Uncertain significance
ubiA 4269502 p.Val111Gly missense_variant 0.18 ethambutol Uncertain significance
aftB 4269504 c.-668A>G upstream_gene_variant 0.19 capreomycin
amikacin
aftB 4269522 c.-686C>T upstream_gene_variant 0.83 capreomycin
amikacin
aftB 4269606 c.-770T>C upstream_gene_variant 0.87 capreomycin
amikacin
ethA 4326465 p.Ile337Val missense_variant 0.79 ethionamide Uncertain significance
whiB6 4338595 c.-75delG upstream_gene_variant 1.0 streptomycin Uncertain significance
capreomycin Uncertain significance
amikacin Uncertain significance
gid 4407588 c.615A>G synonymous_variant 0.86 streptomycin