Run ID: 39bd18c5-1788-4e58-8fca-ef630f8cc97a
Sample name:
Date: 07-05-2024 10:12:29
Number of reads: 4597302
Percentage reads mapped: 97.72
Median coverage: 104
Strain: lineage6.3.1;lineage4.1
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 0.21 |
lineage6 | West-Africa 2 | RD702 | 0.8 |
lineage4.1 | Euro-American | None | 0.12 |
lineage6.3 | West-Africa 2 | RD702 | 0.79 |
lineage6.3.1 | West-Africa 2 | RD702 | 0.8 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Ser315Thr | Assoc w R | |
ethambutol | ||||
pyrazinamide | ||||
moxifloxacin | ||||
levofloxacin | ||||
bedaquiline | ||||
delamanid | ||||
pretomanid | ||||
linezolid | ||||
streptomycin | ||||
amikacin | ||||
kanamycin | ||||
capreomycin | ||||
clofazimine | ||||
ethionamide | ||||
para-aminosalicylic_acid | ||||
cycloserine |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 0.21 | isoniazid | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.81 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
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 | ||||||
fgd1 | 490751 | c.-32T>G | upstream_gene_variant | 0.17 | delamanid | |
fgd1 | 490759 | c.-24A>T | upstream_gene_variant | 0.18 | delamanid | |
fgd1 | 490771 | c.-12T>G | upstream_gene_variant | 0.14 | delamanid | |
fgd1 | 490780 | c.-3C>A | upstream_gene_variant | 0.14 | delamanid | |
fgd1 | 491014 | p.Thr78Pro | missense_variant | 0.18 | delamanid | |
fgd1 | 491668 | p.Lys296Glu | missense_variant | 0.82 | delamanid | Uncertain significance |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.76 | delamanid | |
ccsA | 620551 | p.Asp221His | missense_variant | 0.13 | capreomycin | |
amikacin | ||||||
rpoB | 759611 | c.-196G>C | upstream_gene_variant | 0.15 | rifampicin | |
rpoB | 759615 | c.-192A>C | upstream_gene_variant | 0.3 | rifampicin | |
rpoB | 759620 | c.-187A>C | upstream_gene_variant | 0.23 | rifampicin | |
rpoB | 760969 | p.Ser388Leu | missense_variant | 0.85 | rifampicin | Uncertain significance |
rpoB | 761723 | p.Glu639Asp | missense_variant | 0.89 | rifampicin | Uncertain significance |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 0.83 | rifampicin | |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.15 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.82 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
rplC | 801287 | p.Val160Gly | missense_variant | 0.13 | linezolid | |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 0.79 | delamanid | Uncertain significance |
fbiC | 1303016 | p.Val29Gly | missense_variant | 0.19 | delamanid | |
fbiC | 1304159 | p.Val410Gly | missense_variant | 0.34 | delamanid | |
fbiC | 1304166 | c.1236A>G | synonymous_variant | 0.26 | delamanid | |
fbiC | 1304174 | p.Val415Gly | missense_variant | 0.13 | delamanid | |
Rv1258c | 1407055 | p.Tyr96Asp | missense_variant | 0.12 | streptomycin | |
pyrazinamide | ||||||
isoniazid | ||||||
atpE | 1461251 | c.207G>T | synonymous_variant | 0.81 | bedaquiline | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
inhA | 1674434 | p.Val78Ala | missense_variant | 0.74 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
ndh | 2102694 | p.Val117Ile | missense_variant | 0.83 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
ndh | 2103235 | c.-193C>G | upstream_gene_variant | 0.11 | ethionamide | |
isoniazid | ||||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.74 | isoniazid | Uncertain significance |
katG | 2155503 | c.609C>T | synonymous_variant | 0.83 | isoniazid | |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.79 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.87 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2222852 | p.Ala105Thr | missense_variant | 0.86 | 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 | 0.81 | isoniazid | |
eis | 2714543 | p.Arg264Gly | missense_variant | 0.13 | kanamycin | |
amikacin | ||||||
eis | 2714549 | p.Met262Leu | missense_variant | 0.19 | kanamycin | |
amikacin | ||||||
eis | 2714555 | p.Asp260His | missense_variant | 0.15 | kanamycin | |
amikacin | ||||||
eis | 2714559 | p.Gly258Trp | missense_variant | 0.16 | kanamycin | |
amikacin | ||||||
eis | 2714566 | p.Leu256Pro | missense_variant | 0.15 | kanamycin | Uncertain significance |
amikacin | ||||||
ahpC | 2726338 | p.Val49Gly | missense_variant | 0.13 | isoniazid | |
ahpC | 2726341 | p.Val50Gly | missense_variant | 0.22 | isoniazid | |
ahpC | 2726345 | c.153C>T | synonymous_variant | 0.13 | isoniazid | |
ahpC | 2726350 | p.Trp53Leu | missense_variant | 0.19 | isoniazid | |
thyA | 3074601 | c.-130T>G | upstream_gene_variant | 0.11 | para-aminosalicylic_acid | |
thyA | 3074641 | c.-170C>T | 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 | 0.84 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.98 | cycloserine | |
ald | 3086856 | p.Glu13Lys | missense_variant | 0.85 | cycloserine | |
ald | 3087084 | c.266delA | frameshift_variant | 0.79 | cycloserine | |
fbiD | 3339273 | c.156T>G | synonymous_variant | 0.11 | delamanid | |
Rv3083 | 3449781 | c.1278G>A | synonymous_variant | 0.74 | ethionamide | |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
fprA | 3475159 | p.Asn385Asp | missense_variant | 0.79 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
Rv3236c | 3612835 | c.282T>G | synonymous_variant | 0.14 | pyrazinamide | |
rpoA | 3877696 | p.Thr271Ile | missense_variant | 0.82 | rifampicin | Uncertain significance |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.78 | ethambutol | Uncertain significance |
embC | 4241843 | p.Leu661Ile | missense_variant | 0.78 | ethambutol | Uncertain significance |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
embC | 4242803 | p.Val981Leu | missense_variant | 0.41 | ethambutol | Uncertain significance |
embA | 4244220 | c.988C>T | synonymous_variant | 0.69 | ethambutol | |
embA | 4244379 | p.Pro383Ser | missense_variant | 0.6 | ethambutol | Uncertain significance |
embB | 4246864 | c.351C>T | synonymous_variant | 0.78 | ethambutol | |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.65 | ethambutol | Uncertain significance |
embB | 4249298 | p.Trp929Gly | missense_variant | 0.17 | ethambutol | |
embB | 4249305 | p.Asn931Thr | missense_variant | 0.18 | ethambutol | |
embB | 4249323 | p.Ala937Glu | missense_variant | 0.29 | ethambutol | |
aftB | 4268477 | c.360C>T | synonymous_variant | 0.77 | capreomycin | |
amikacin | ||||||
aftB | 4268776 | p.Ser21Gly | missense_variant | 0.2 | capreomycin | |
amikacin | Uncertain significance | |||||
aftB | 4269351 | c.-515C>T | upstream_gene_variant | 0.85 | capreomycin | |
amikacin | ||||||
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.87 | ethambutol | Uncertain significance |
ubiA | 4269502 | p.Val111Gly | missense_variant | 0.14 | ethambutol | Uncertain significance |
aftB | 4269504 | c.-668A>G | upstream_gene_variant | 0.14 | capreomycin | |
amikacin | ||||||
aftB | 4269522 | c.-686C>T | upstream_gene_variant | 0.79 | capreomycin | |
amikacin | ||||||
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 0.88 | capreomycin | |
amikacin | ||||||
ethA | 4326465 | p.Ile337Val | missense_variant | 0.86 | 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 | 0.78 | streptomycin | |
gid | 4408327 | c.-125A>G | upstream_gene_variant | 0.79 | streptomycin |