Run ID: ERR551342
Sample name:
Date: 2024-03-26T16:13:49.869354
Number of reads: 1257895
Percentage reads mapped: 99.59
Median coverage: 41.0
Strain: lineage4.1.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 0.99 |
lineage4.1.2 | Euro-American | None | 1.0 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | c.1293_1295dupCCA | Assoc w R - Interim | |
c.1293_1295dupCCA | Mutation from literature | |||
isoniazid | katG | c.1286_1288delCGC | Mutation from literature | |
ethambutol | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | c.-12T>C | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-12C>T | Assoc w R | |
c.-15C>G | Uncertain significance | Mutation from literature | ||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761098 | c.1293_1295dupCCA | disruptive_inframe_insertion | 1.0 | rifampicin | Assoc w R - Interim | |
rifampicin | Mutation from literature | ||||||
katG | 2154823 | c.1286_1288delCGC | disruptive_inframe_deletion | 1.0 | isoniazid | Mutation from literature | |
pncA | 2289253 | c.-12T>C | upstream_gene_variant | 0.68 | pyrazinamide | Assoc w R | |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 0.67 | kanamycin | Assoc w R | |
eis | 2715347 | c.-15C>G | upstream_gene_variant | 0.33 | kanamycin | Uncertain significance | Mutation from literature |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | 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 | 491591 | p.Lys270Met | missense_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 1.0 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoB | 760115 | c.309C>T | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | 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 |
embR | 1418031 | c.-684G>A | upstream_gene_variant | 1.0 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
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 |
bacA | 2064664 | c.64dupT | frameshift_variant | 0.42 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2289144 | p.Asp33Val | missense_variant | 0.44 | pyrazinamide | |
pncA | 2289153 | p.Ala30Val | missense_variant | 0.46 | pyrazinamide | Uncertain significance |
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 | isoniazid | |
eis | 2714479 | p.Ala285Val | missense_variant | 1.0 | amikacin | Uncertain significance |
kanamycin | ||||||
Rv2680 | 2996136 | p.Ser11Asn | missense_variant | 0.19 | capreomycin | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
embC | 4239298 | c.-565C>T | upstream_gene_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | ethambutol | Not assoc w R |
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 | 4407793 | p.Arg137Pro | missense_variant | 1.0 | streptomycin | Uncertain significance |