Run ID: SRR25827804
Sample name:
Date: 2024-10-04T22:39:43.158238
Number of reads: 15956542
Percentage reads mapped: 99.23
Median coverage: 539.5
Strain: lineage2.2.1;lineage3.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.45 |
lineage2 | East-Asian | RD105 | 0.53 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.54 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.54 |
lineage3.1 | East-African-Indian | RD750 | 0.41 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Met306Val | Assoc w R | |
p.Gln497Arg | Assoc w R | |||
pyrazinamide | pncA | p.Trp68Leu | Assoc w R - Interim | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
p.Lys88Arg | Assoc w R | |||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Ser91Pro | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
p.Asp94Asn | Assoc w R | High-level resistance | ||
ofloxacin | ||||
levofloxacin | gyrA | p.Ser91Pro | Assoc w R | |
p.Asp94Asn | Assoc w R | |||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.57 | 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) | |||||
gyrA | 7581 | p.Asp94Asn | missense_variant | 0.43 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.57 | streptomycin | Assoc w R | |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.43 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.45 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289039 | p.Trp68Leu | missense_variant | 0.44 | pyrazinamide | Assoc w R - Interim | |
embB | 4247429 | p.Met306Val | missense_variant | 0.48 | ethambutol | Assoc w R | |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.47 | ethambutol | 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 | |||||
gyrA | 9788 | c.2487C>T | synonymous_variant | 0.47 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
fgd1 | 491290 | p.Val170Met | missense_variant | 0.58 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.55 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.54 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.56 | ethionamide | Uncertain significance |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.42 | rifampicin | Not assoc w R |
rpoB | 761557 | p.Ala584Asp | missense_variant | 0.53 | rifampicin | Uncertain significance |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.49 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 764817 | p.Val483Ala | missense_variant | 0.44 | rifampicin | Uncertain significance |
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 | 776182 | p.Asp767Asn | missense_variant | 0.46 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.55 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1253930 | p.Phe202Tyr | missense_variant | 0.57 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
fbiC | 1303428 | c.498C>A | synonymous_variant | 0.44 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
fbiC | 1304265 | c.1335C>T | synonymous_variant | 0.41 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.54 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rpsA | 1833494 | c.-48T>C | upstream_gene_variant | 0.46 | pyrazinamide | Uncertain significance |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.58 | 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 | |||||
pncA | 2288758 | p.Gly162Arg | missense_variant | 0.57 | pyrazinamide | Uncertain significance |
pncA | 2289047 | c.195C>T | synonymous_variant | 0.43 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.45 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.42 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.41 | 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 | |||||
Rv2477c | 2784211 | c.-169A>C | upstream_gene_variant | 0.2 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.52 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.51 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
fbiB | 3642005 | c.471C>G | synonymous_variant | 0.46 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.45 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.45 | 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 | 4241022 | p.Ala387Val | missense_variant | 0.55 | ethambutol | Uncertain significance |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.46 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.5 | ethambutol | Not assoc w R |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.18 | ethambutol | |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.55 | ethambutol | Not assoc w R |
ethA | 4326912 | p.Val188Ile | missense_variant | 0.5 | ethionamide | 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 | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
gid | 4407620 | p.Tyr195His | missense_variant | 0.47 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.54 | streptomycin | Not assoc w R |