Run ID: SRR1180361
Sample name:
Date: 2024-10-03T16:08:53.362404
Number of reads: 2881486
Percentage reads mapped: 99.56
Median coverage: 63.0
Strain: lineage2.2.1;lineage4.1.2;lineage4.8
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.46 |
lineage4.1 | Euro-American | None | 0.24 |
lineage4.1.2 | Euro-American | None | 0.28 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.45 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.47 |
lineage4 | Euro-American | None | 0.52 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.27 |
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 |
---|---|---|---|---|---|---|
dnaA | 371 | p.Pro124Leu | missense_variant | 0.22 | isoniazid | Not assoc w R |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.71 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.69 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491100 | c.318C>T | synonymous_variant | 0.31 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
fgd1 | 491556 | c.774G>A | synonymous_variant | 0.55 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.43 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.42 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.52 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.44 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.48 | ethionamide | Uncertain significance |
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.19 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.44 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.24 | 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 | 0.49 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.45 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.39 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.49 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.37 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embR | 1417140 | p.Ala70Ser | missense_variant | 0.23 | ethambutol | Not assoc w R |
embR | 1418018 | c.-671C>T | upstream_gene_variant | 0.23 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
inhA | 1673249 | c.-953C>T | upstream_gene_variant | 0.22 | isoniazid | |
ethionamide | ||||||
inhA | 1674210 | c.9A>C | synonymous_variant | 0.4 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R - Interim | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.48 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.65 | 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 | 0.46 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.44 | pyrazinamide | Not assoc w R |
PPE35 | 2168524 | p.Gly697Ser | missense_variant | 0.34 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
folC | 2747022 | p.Val193Ile | missense_variant | 0.2 | para-aminosalicylic_acid | |
Rv2477c | 2783944 | p.Lys33Asn | missense_variant | 0.4 | kanamycin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
Rv2752c | 3064519 | c.1672delG | frameshift_variant | 0.42 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.66 | cycloserine | |
Rv3083 | 3448894 | p.Tyr131Asp | missense_variant | 0.43 | ethionamide | Uncertain significance |
Rv3083 | 3449642 | p.Asn380Ser | missense_variant | 0.43 | ethionamide | Uncertain significance |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.48 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.78 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625403 | p.Val404Ala | missense_variant | 0.27 | rifampicin | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.51 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
fbiA | 3641164 | p.Ile208Val | missense_variant | 0.16 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
alr | 3840764 | c.657G>C | synonymous_variant | 0.29 | cycloserine | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.25 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.47 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.4 | ethambutol | Not assoc w R |
aftB | 4268861 | c.-25T>C | upstream_gene_variant | 0.29 | ethambutol | Uncertain significance |
whiB6 | 4338286 | p.Val79Ala | missense_variant | 0.5 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
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 | 0.74 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.47 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.42 | streptomycin | Not assoc w R |