Run ID: SRR5153240
Sample name:
Date: 2024-10-03T20:48:52.644686
Number of reads: 3456031
Percentage reads mapped: 99.23
Median coverage: 71.0
Strain: lineage4.1.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 1.0 |
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 | p.Asp435Tyr | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Gln497Arg | Assoc w R | |
p.Asp1024Asn | Uncertain significance | Mutation from literature | ||
pyrazinamide | pncA | p.Ile5Thr | Uncertain significance | Mutation from literature |
streptomycin | gid | c.102delG | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
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 | |
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761109 | p.Asp435Tyr | missense_variant | 1.0 | rifampicin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289228 | p.Ile5Thr | missense_variant | 1.0 | pyrazinamide | Uncertain significance | Mutation from literature |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.99 | ethambutol | Assoc w R | |
embB | 4249583 | p.Asp1024Asn | missense_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
gid | 4408100 | c.102delG | frameshift_variant | 1.0 | streptomycin | 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 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Not assoc w R | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 1.0 | isoniazid | Not assoc w R |
ethionamide | 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 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781276 | c.-284A>C | upstream_gene_variant | 1.0 | streptomycin | |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800485 | c.-324G>A | upstream_gene_variant | 1.0 | linezolid | Uncertain significance |
embR | 1417196 | p.Gly51Glu | missense_variant | 1.0 | ethambutol | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
tsnR | 1853447 | c.-159C>T | upstream_gene_variant | 1.0 | linezolid | |
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 1.0 | isoniazid | |
Rv2680 | 2996085 | c.-20G>A | upstream_gene_variant | 0.26 | capreomycin | Uncertain significance |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4039672 | p.Val345Leu | missense_variant | 0.98 | pyrazinamide | Uncertain significance |
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 |
ethA | 4326209 | p.Pro422Leu | missense_variant | 1.0 | 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 |