Run ID: SRR13837864
Sample name:
Date: 2024-04-16T03:24:51.572011
Number of reads: 2951535
Percentage reads mapped: 96.43
Median coverage: 100.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | embC | p.Tyr296His | Mutation from literature | |
embB | p.Met482Ile | Mutation from literature | ||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | mmpR5 | p.Tyr26* | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | mmpR5 | p.Tyr26* | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
mmpR5 | 779067 | p.Tyr26* | stop_gained | 1.0 | bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | |||||
embC | 4240748 | p.Tyr296His | missense_variant | 1.0 | ethambutol | Mutation from literature | |
embB | 4247959 | p.Met482Ile | missense_variant | 0.99 | ethambutol | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
fgd1 | 491360 | p.Ile193Ser | missense_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
mshA | 576396 | p.Ser350Ile | missense_variant | 1.0 | ethionamide | |
isoniazid | ||||||
rpoB | 760225 | p.Glu140Ala | missense_variant | 0.98 | rifampicin | |
rpoC | 767186 | p.Gln1273* | stop_gained | 0.99 | rifampicin | |
rplC | 800933 | p.Pro42His | missense_variant | 1.0 | linezolid | |
fbiC | 1305306 | c.2376A>T | synonymous_variant | 0.99 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
tlyA | 1918560 | c.621G>T | synonymous_variant | 1.0 | capreomycin | |
bacA | 2063120 | c.1609C>T | synonymous_variant | 1.0 | streptomycin | Not assoc w R - Interim |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
ndh | 2102402 | p.Leu214Arg | missense_variant | 1.0 | ethionamide | |
delamanid | ||||||
isoniazid | Uncertain significance | |||||
katG | 2156175 | c.-64T>G | upstream_gene_variant | 1.0 | isoniazid | |
PPE35 | 2169349 | p.Phe422Ile | missense_variant | 1.0 | pyrazinamide | |
PPE35 | 2170540 | p.Leu25Val | missense_variant | 1.0 | pyrazinamide | |
pncA | 2288999 | p.Phe81Leu | missense_variant | 1.0 | pyrazinamide | |
fbiD | 3339660 | c.543C>G | synonymous_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
Rv3236c | 3612627 | p.Ala164Thr | missense_variant | 1.0 | pyrazinamide | |
fbiA | 3640219 | c.-324C>T | upstream_gene_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
embA | 4244119 | p.Tyr296Phe | missense_variant | 1.0 | ethambutol | |
embB | 4247417 | p.Tyr302Asn | missense_variant | 0.98 | ethambutol | |
embB | 4248036 | p.Val508Gly | missense_variant | 0.99 | ethambutol | |
embB | 4248325 | c.1812G>C | synonymous_variant | 1.0 | ethambutol | |
aftB | 4267894 | p.Ile315Phe | missense_variant | 1.0 | ethambutol | |
ethA | 4326052 | p.Asp474Glu | missense_variant | 1.0 | ethionamide | |
ethA | 4327388 | p.Thr29Ile | missense_variant | 1.0 | ethionamide | |
ethR | 4328162 | p.His205Pro | missense_variant | 1.0 | ethionamide | |
whiB6 | 4338518 | c.4C>A | synonymous_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin |