Run ID: ERR4810570
Sample name:
Date: 2024-04-16T09:52:22.971206
Number of reads: 6178088
Percentage reads mapped: 98.99
Median coverage: 185.0
Strain: lineage2.2.1;lineage4.5
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.5 | Euro-American | RD122 | 0.52 |
lineage2 | East-Asian | RD105 | 0.48 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.5 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.5 |
lineage4 | Euro-American | None | 0.51 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|
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 | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7892 | c.591G>A | synonymous_variant | 0.57 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13569 | c.-11C>T | upstream_gene_variant | 0.47 | isoniazid | Uncertain significance |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.55 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
ccsA | 620029 | c.139C>T | synonymous_variant | 0.56 | capreomycin | Not assoc w R - Interim |
amikacin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.52 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.45 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.43 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.52 | rifampicin | Not assoc w R |
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 | 0.54 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776312 | p.Glu723Asp | missense_variant | 0.51 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpL5 | 778243 | p.Lys80Gln | missense_variant | 0.51 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.51 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 801426 | c.618C>T | synonymous_variant | 0.54 | linezolid | |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.5 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
fbiC | 1302927 | c.-4C>T | upstream_gene_variant | 0.49 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.43 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
inhA | 1674043 | c.-159G>T | upstream_gene_variant | 0.51 | ethionamide | |
isoniazid | Uncertain significance | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.47 | 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 | 0.52 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.47 | pyrazinamide | Not assoc w R |
PPE35 | 2169242 | c.1370delG | frameshift_variant | 0.55 | pyrazinamide | Uncertain significance |
PPE35 | 2170030 | c.549_582delGGCCGTGGTGACCGCGCTCACCACGGCCGTGGGC | frameshift_variant | 0.44 | pyrazinamide | Uncertain significance |
PPE35 | 2170568 | p.Ile15Met | missense_variant | 0.53 | 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 | |||||
Rv2477c | 2782403 | p.Pro547Leu | missense_variant | 0.46 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
Rv2752c | 3065129 | c.1063C>T | synonymous_variant | 0.48 | ethambutol | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
thyX | 3067975 | c.-30C>T | upstream_gene_variant | 0.54 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.54 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.42 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3624398 | c.513C>T | synonymous_variant | 0.54 | bedaquiline | Not assoc w R - Interim |
rifampicin | 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 | 0.45 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 0.42 | rifampicin | Not assoc w R |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 0.55 | pyrazinamide | Not assoc w R |
embC | 4239046 | c.-817T>G | upstream_gene_variant | 0.47 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.48 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.52 | ethambutol | Not assoc w R |
aftB | 4268495 | c.342G>C | synonymous_variant | 0.53 | ethambutol | Not assoc w R - Interim |
ethA | 4326676 | p.Ser266Arg | missense_variant | 0.49 | ethionamide | Uncertain significance |
ethA | 4326937 | c.537C>T | synonymous_variant | 0.51 | ethionamide | Not assoc w R - Interim |
whiB6 | 4338359 | p.Ala55Pro | missense_variant | 0.4 | 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 | 0.51 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.45 | streptomycin | Not assoc w R |