Run ID: ERR4799888
Sample name:
Date: 2024-04-15T09:18:52.135837
Number of reads: 2870171
Percentage reads mapped: 99.5
Median coverage: 68.0
Strain: lineage2.2.1;lineage3
Spoligotype:
Drug-resistance: XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.57 |
lineage2 | East-Asian | RD105 | 0.46 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.43 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.41 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | mmpR5 | c.144dupC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | mmpR5 | c.144dupC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
linezolid | rplC | p.Cys154Arg | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.39 | moxifloxacin | Assoc w R | High-level resistance |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.57 | rifampicin | Assoc w R | |
mmpR5 | 779130 | c.144dupC | frameshift_variant | 0.24 | clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | |||||
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.54 | streptomycin | Assoc w R | |
rplC | 801268 | p.Cys154Arg | missense_variant | 0.55 | linezolid | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.42 | isoniazid | Assoc w R | High-level resistance |
embB | 4247429 | p.Met306Val | missense_variant | 0.45 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.97 | 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 | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.98 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.56 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620553 | c.663T>C | synonymous_variant | 0.26 | capreomycin | Not assoc w R |
amikacin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.41 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.94 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.32 | ethionamide | Uncertain significance |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.46 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.62 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 764817 | p.Val483Ala | missense_variant | 0.46 | rifampicin | Uncertain significance |
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 | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.47 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.47 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.35 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1473609 | n.-49G>C | upstream_gene_variant | 0.39 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.35 | pyrazinamide | Not assoc w R - Interim |
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 |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 0.52 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.5 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.52 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.57 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.98 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.52 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.41 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3640211 | c.-332T>G | upstream_gene_variant | 0.45 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
rpoA | 3879096 | c.-589C>T | upstream_gene_variant | 0.24 | rifampicin | |
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.67 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.5 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embC | 4240067 | p.Ser69Val | missense_variant | 0.41 | ethambutol | |
embC | 4242056 | p.Pro732Ala | missense_variant | 0.51 | ethambutol | Uncertain significance |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.43 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 0.98 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.49 | ethambutol | Not assoc w R |
embB | 4249757 | p.Thr1082Ala | missense_variant | 0.52 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.32 | ethambutol | Not assoc w R |
whiB6 | 4338356 | c.161_165dupGGGCT | frameshift_variant | 0.34 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
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 | 1.0 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.35 | streptomycin | Not assoc w R |