Run ID: SRR15316381
Sample name:
Date: 2024-10-05T10:21:44.087797
Number of reads: 9327469
Percentage reads mapped: 99.57
Median coverage: 286.0
Strain: lineage2.2.1;lineage4.4.2;lineage4.5
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.5 | Euro-American | RD122 | 0.21 |
lineage2 | East-Asian | RD105 | 0.64 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.63 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.64 |
lineage4 | Euro-American | None | 0.36 |
lineage4.4 | Euro-American | None | 0.18 |
lineage4.4.2 | Euro-American | None | 0.16 |
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 | 0.24 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7914 | c.613C>T | synonymous_variant | 0.14 | 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 | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.69 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.6 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
ccsA | 620029 | c.139C>T | synonymous_variant | 0.2 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.57 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.64 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.68 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.6 | 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 | 0.64 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.63 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.67 | 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 | 0.64 | 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 | 0.65 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
Rv1258c | 1407380 | c.-40C>T | upstream_gene_variant | 0.18 | streptomycin | Uncertain significance |
pyrazinamide | ||||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1471820 | n.-26T>G | upstream_gene_variant | 0.16 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rpsA | 1833410 | c.-132G>A | upstream_gene_variant | 0.15 | pyrazinamide | |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.64 | 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 | 0.59 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.54 | pyrazinamide | Not assoc w R |
PPE35 | 2170568 | p.Ile15Met | missense_variant | 0.2 | pyrazinamide | Not assoc w R |
Rv1979c | 2222090 | p.Leu359Met | missense_variant | 0.17 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2222510 | p.Ser219Ala | missense_variant | 0.16 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2752c | 3065478 | p.Phe238Leu | missense_variant | 0.32 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
Rv2752c | 3066099 | p.Met31Ile | missense_variant | 0.18 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.79 | cycloserine | |
fbiD | 3339480 | p.Gln121His | missense_variant | 0.17 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
Rv3083 | 3448348 | c.-156G>A | upstream_gene_variant | 0.11 | ethionamide | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.6 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3624850 | p.Ser21Gly | missense_variant | 0.16 | rifampicin | |
bedaquiline | ||||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.67 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
rpoA | 3878575 | c.-68C>T | upstream_gene_variant | 0.17 | rifampicin | Not assoc w R |
clpC1 | 4038318 | p.Pro796Leu | missense_variant | 0.17 | pyrazinamide | Not assoc w R |
embC | 4238963 | c.-900C>T | upstream_gene_variant | 0.19 | ethambutol | Not assoc w R |
embC | 4240629 | p.Gly256Asp | missense_variant | 0.33 | ethambutol | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243458 | p.Cys76Gly | missense_variant | 0.15 | ethambutol | |
embA | 4243482 | p.Ala84Ser | missense_variant | 0.17 | ethambutol | Uncertain significance |
embA | 4246508 | c.3276G>A | synonymous_variant | 0.14 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.61 | ethambutol | Not assoc w R |
ubiA | 4268928 | c.906C>T | synonymous_variant | 0.12 | ethambutol | Not assoc w R |
ubiA | 4269375 | c.459G>A | synonymous_variant | 0.14 | ethambutol | Not assoc w R |
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 | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.63 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.63 | streptomycin | Not assoc w R |