Run ID: 85781ee9-f6db-48b7-8d13-fa5dc0b09b2f
Sample name:
Date: 03-10-2023 13:59:07
Number of reads: 4301699
Percentage reads mapped: 99.22
Median coverage: 142
Strain: lineage2.2.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | |
ethambutol | embB | p.Gly406Asp | Assoc w R | |
pyrazinamide | pncA | p.Cys14Arg | Assoc w R | |
moxifloxacin | gyrA | p.Ser91Pro | Assoc w R | |
levofloxacin | gyrA | p.Ser91Pro | Assoc w R | |
bedaquiline | ||||
delamanid | ||||
pretomanid | ||||
linezolid | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
amikacin | ||||
kanamycin | ||||
capreomycin | ||||
clofazimine | ||||
ethionamide | ||||
para-aminosalicylic_acid | thyX | c.-16C>T | Uncertain significance | |
thyA | p.Arg222Gly | Uncertain significance | ||
cycloserine |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 1.0 | ofloxacin | Uncertain significance | |
moxifloxacin | Assoc w R | ||||||
levofloxacin | Assoc w R | ||||||
fluoroquinolones | Uncertain significance | ||||||
ciprofloxacin | Uncertain significance | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | |
pncA | 2289202 | p.Cys14Arg | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | Uncertain significance | |
thyA | 3073808 | p.Arg222Gly | missense_variant | 1.0 | para-aminosalicylic_acid | Uncertain significance | |
embB | 4247730 | p.Gly406Asp | missense_variant | 1.0 | ethambutol | Assoc w R |
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 | 0.99 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.99 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | delamanid | |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
mshA | 576108 | p.Ala254Gly | missense_variant | 0.22 | ethionamide | Uncertain significance |
isoniazid | ||||||
ccsA | 620625 | p.Ile245Met | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 | rifampicin | |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 766779 | p.Glu1137Gly | missense_variant | 1.0 | rifampicin | |
rpoC | 767120 | p.Asn1251Asp | missense_variant | 0.56 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
rrl | 1476091 | n.2434T>C | non_coding_transcript_exon_variant | 1.0 | linezolid | Uncertain significance |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | pyrazinamide | |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
PPE35 | 2170065 | p.Ala183Gly | missense_variant | 0.3 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
pepQ | 2860159 | p.Ala87Gly | missense_variant | 0.18 | clofazimine | |
bedaquiline | ||||||
thyA | 3074345 | p.Pro43Ser | missense_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.76 | delamanid | |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
fbiB | 3641810 | c.276G>C | synonymous_variant | 1.0 | delamanid | |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 | ethambutol | |
embB | 4246544 | p.Thr11Pro | missense_variant | 0.15 | ethambutol | Uncertain significance |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.14 | ethambutol | |
embB | 4248324 | p.Ala604Gly | missense_variant | 0.21 | ethambutol | |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
aftB | 4268619 | p.Val73Gly | missense_variant | 0.24 | capreomycin | |
amikacin | ||||||
ethA | 4326339 | p.Asn379Asp | missense_variant | 1.0 | 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 | 1.0 | streptomycin | |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.99 | streptomycin | Uncertain significance |