Run ID: SRR28385876
Sample name:
Date: 2025-02-27T19:24:21.376422
Number of reads: 3970788
Percentage reads mapped: 98.74
Median coverage: 133.0
Strain: lineage2.2.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 1.0 |
lineage2.2.2 | East-Asian (Beijing) | RD105;RD207 | 0.99 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ile491Phe | Assoc w R | |
rpoC | p.Asp735Asn | Uncertain significance | Mutation from literature | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
p.Asn238Lys | Mutation from literature | |||
ethambutol | embB | p.Asp354Ala | Assoc w R | |
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-12C>T | Assoc w R | |
cycloserine | ||||
ethionamide | ethA | p.Arg279* | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.68 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
rpoB | 761277 | p.Ile491Phe | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpoC | 765572 | p.Asp735Asn | missense_variant | 1.0 | rifampicin | Uncertain significance | Mutation from literature |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
katG | 2155398 | p.Asn238Lys | missense_variant | 1.0 | isoniazid | Mutation from literature | |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 1.0 | kanamycin | Assoc w R | |
embB | 4247574 | p.Asp354Ala | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4326639 | p.Arg279* | stop_gained | 0.62 | ethionamide | Assoc w R |
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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
delamanid | Not assoc w R - Interim | |||||
pretomanid | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | 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 | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 779022 | c.-542G>A | upstream_gene_variant | 0.99 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rpsL | 781406 | c.-154_-153insC | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
Rv1129c | 1254039 | p.Asn166Asp | missense_variant | 1.0 | isoniazid | Uncertain significance |
levofloxacin | Uncertain significance | |||||
moxifloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
levofloxacin | Not assoc w R | |||||
moxifloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | amikacin | Uncertain significance |
capreomycin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rpsA | 1833909 | p.Asp123Ala | missense_variant | 0.98 | pyrazinamide | Uncertain significance |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | 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 | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | 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 | |||||
Rv2477c | 2782899 | p.Glu382Lys | missense_variant | 0.99 | amikacin | Uncertain significance |
ethambutol | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
moxifloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
thyA | 3074495 | c.-24C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | Uncertain significance |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | Uncertain significance |
whiB7 | 3568425 | c.255T>G | synonymous_variant | 0.22 | amikacin | Uncertain significance |
kanamycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
Rv3236c | 3612069 | p.Gly350Arg | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.99 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3640371 | c.-172G>T | upstream_gene_variant | 0.49 | clofazimine | Uncertain significance |
delamanid | Uncertain significance | |||||
pretomanid | Uncertain significance | |||||
ddn | 3987084 | p.Gly81Ser | missense_variant | 1.0 | delamanid | Uncertain significance |
pretomanid | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4327286 | p.Gly63Asp | missense_variant | 0.29 | ethionamide | Uncertain significance |
whiB6 | 4338473 | c.49A>C | synonymous_variant | 1.0 | amikacin | Not assoc w R - Interim |
capreomycin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | amikacin | Not assoc w R |
capreomycin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | amikacin | Uncertain significance |
capreomycin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 1.0 | streptomycin | Not assoc w R |