Run ID: SRR25827394
Sample name:
Date: 2024-10-04T01:14:13.714583
Number of reads: 2763688
Percentage reads mapped: 99.19
Median coverage: 88.0
Strain: lineage2.2.1;lineage3;lineage4.9
Spoligotype:
Drug-resistance: XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.05 |
lineage2 | East-Asian | RD105 | 0.65 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.68 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.64 |
lineage4 | Euro-American | None | 0.27 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.15 |
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.Gly132Ala | Assoc w R | |
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) |
p.Asp94Gly | Assoc w R | High-level resistance | ||
ofloxacin | ||||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
p.Asp94Gly | Assoc w R | |||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
kanamycin | rrs | n.1401A>G | Assoc w R | |
eis | c.-10G>C | Uncertain significance | Mutation from literature | |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid | rplC | p.Cys154Arg | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.49 | 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 | 7582 | p.Asp94Gly | missense_variant | 0.25 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.76 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.63 | streptomycin | Assoc w R | |
rplC | 801268 | p.Cys154Arg | missense_variant | 0.21 | linezolid | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.45 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.24 | 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 | 0.92 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288847 | p.Gly132Ala | missense_variant | 0.16 | pyrazinamide | Assoc w R | |
eis | 2715342 | c.-10G>C | upstream_gene_variant | 0.19 | kanamycin | Uncertain significance | Mutation from literature |
embB | 4247429 | p.Met306Val | missense_variant | 0.26 | ethambutol | Assoc w R | |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.31 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.81 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.77 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.78 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491290 | p.Val170Met | missense_variant | 0.51 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.79 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.57 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.56 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.67 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.63 | ethionamide | Uncertain significance |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.75 | rifampicin | Not assoc w R |
rpoC | 764840 | p.Ile491Val | missense_variant | 0.4 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.84 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.72 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.65 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.65 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.88 | streptomycin | Not assoc w R |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 0.14 | linezolid | |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.72 | 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 | 0.74 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.89 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.74 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.98 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 0.8 | capreomycin | Not assoc w R |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.74 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.84 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.89 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.89 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.66 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.8 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.55 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
embC | 4240413 | p.Leu184Arg | missense_variant | 0.13 | ethambutol | |
embC | 4241022 | p.Ala387Val | missense_variant | 0.34 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 0.86 | ethambutol | Not assoc w R |
embA | 4243190 | c.-43G>C | upstream_gene_variant | 0.14 | ethambutol | Uncertain significance |
embA | 4243460 | c.228C>T | synonymous_variant | 0.58 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.67 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 0.86 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 0.81 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.71 | streptomycin | Not assoc w R |
gid | 4407620 | p.Tyr195His | missense_variant | 0.45 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.58 | streptomycin | Not assoc w R |