Run ID: ERR4799020
Sample name:
Date: 2024-10-05T05:55:58.488031
Number of reads: 2992379
Percentage reads mapped: 99.62
Median coverage: 86.0
Strain: lineage3.1.2;lineage4.8
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.38 |
lineage3.1.2 | East-African-Indian | RD750 | 0.32 |
lineage4 | Euro-American | None | 0.62 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.56 |
lineage3.1 | East-African-Indian | RD750 | 0.28 |
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 | 0.48 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.49 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.45 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.3 | ethionamide | Not assoc w R - Interim |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.38 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.4 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.4 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.37 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpR5 | 779352 | c.363G>A | synonymous_variant | 0.22 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.42 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
Rv1129c | 1254620 | c.-86C>T | upstream_gene_variant | 0.59 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
fbiC | 1303928 | p.Ala333Val | missense_variant | 0.23 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
Rv1258c | 1406897 | c.444G>A | synonymous_variant | 0.28 | streptomycin | Not assoc w R - Interim |
pyrazinamide | ||||||
isoniazid | Not assoc w R - Interim | |||||
rrs | 1471522 | n.-324T>G | upstream_gene_variant | 0.41 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.49 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rrl | 1474429 | n.772G>A | non_coding_transcript_exon_variant | 0.54 | capreomycin | |
linezolid | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.37 | 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 | 0.37 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.41 | pyrazinamide | Not assoc w R |
PPE35 | 2168604 | p.Pro670Leu | missense_variant | 0.36 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223491 | c.-327C>A | upstream_gene_variant | 0.55 | bedaquiline | Uncertain significance |
clofazimine | Not assoc w R | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 0.38 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.38 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.37 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.29 | kanamycin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.33 | cycloserine | |
whiB7 | 3568968 | c.-289G>A | upstream_gene_variant | 0.23 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
Rv3236c | 3613255 | c.-139G>A | upstream_gene_variant | 0.29 | pyrazinamide | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.39 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.42 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.4 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
embC | 4242075 | p.Arg738Gln | missense_variant | 0.44 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4246811 | p.Gly100Ser | missense_variant | 0.55 | ethambutol | Uncertain significance |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.1 | ethambutol | Not assoc w R |
whiB6 | 4338401 | p.Trp41Arg | missense_variant | 0.54 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 0.43 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.41 | streptomycin | Not assoc w R |