Run ID: SRR25827805
Sample name:
Date: 2024-04-14T18:09:49.946084
Number of reads: 3149888
Percentage reads mapped: 49.87
Median coverage: 90.0
Strain: lineage3.1.3
Spoligotype:
Drug-resistance: XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.99 |
lineage3.1.3 | East-African-Indian | RD750 | 0.68 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Asn | Assoc w R | |
p.Ser450Leu | Assoc w R | |||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
p.Thr275Ala | Uncertain significance | Mutation from literature | ||
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | c.395delG | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-10G>A | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
cycloserine | ||||
ethionamide | ||||
clofazimine | mmpR5 | c.36delC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | mmpR5 | c.36delC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.34 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761139 | p.His445Asn | missense_variant | 0.62 | rifampicin | Assoc w R | |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.4 | rifampicin | Assoc w R | |
mmpR5 | 779023 | c.36delC | frameshift_variant | 0.72 | bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.25 | isoniazid | Assoc w R | High-level resistance |
katG | 2155289 | p.Thr275Ala | missense_variant | 0.24 | isoniazid | Uncertain significance | Mutation from literature |
pncA | 2288846 | c.395delG | frameshift_variant | 0.23 | pyrazinamide | Assoc w R | |
eis | 2715342 | c.-10G>A | upstream_gene_variant | 0.3 | kanamycin | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
embB | 4247429 | p.Met306Val | missense_variant | 0.32 | 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 | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
nusG | 734261 | p.Thr3Asn | missense_variant | 0.61 | rifampicin | Not assoc w R |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.23 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.99 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765862 | p.Phe831Leu | missense_variant | 0.22 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
Rv1258c | 1406613 | p.Glu243Ala | missense_variant | 0.75 | streptomycin | Uncertain significance |
isoniazid | Not assoc w R | |||||
pyrazinamide | Not assoc w R | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834159 | c.618G>A | synonymous_variant | 0.67 | pyrazinamide | Not assoc w R |
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 | 2154194 | c.1917_1918insGCG | conservative_inframe_insertion | 0.65 | isoniazid | |
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 | 2222732 | c.432delT | frameshift_variant | 0.74 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 0.24 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.97 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
thyA | 3073687 | p.Ala262Val | missense_variant | 0.22 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
lpqB | 3623174 | c.1737G>C | synonymous_variant | 0.35 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3841473 | c.-53G>A | upstream_gene_variant | 0.23 | cycloserine | |
panD | 4044872 | c.-591C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.28 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249195 | c.2682C>A | synonymous_variant | 0.66 | ethambutol | Not assoc w R |
aftB | 4267492 | p.Ala449Thr | missense_variant | 0.24 | ethambutol | Uncertain significance |
ethA | 4327076 | p.Phe133Ser | missense_variant | 0.27 | ethionamide | Uncertain significance |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
gid | 4408114 | p.Gly30Asp | missense_variant | 0.26 | streptomycin | Uncertain significance |
gid | 4408175 | p.Ala10Pro | missense_variant | 0.76 | streptomycin | Uncertain significance |