Run ID: SRR1202535
Sample name:
Date: 2024-03-26T12:12:49.146950
Number of reads: 3358073
Percentage reads mapped: 98.63
Median coverage: 42.0
Strain: lineage4
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Asn499Asp | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrB | p.Asn499Asp | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6734 | p.Asn499Asp | missense_variant | 0.13 | moxifloxacin | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
levofloxacin | 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 | 8147 | p.Asn282Lys | missense_variant | 0.99 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13339 | c.219delG | frameshift_variant | 1.0 | isoniazid | Uncertain significance |
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 | 0.99 | streptomycin | Not assoc w R |
fbiC | 1304501 | p.Ala524Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
fbiC | 1304721 | c.1791C>G | synonymous_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fbiC | 1305357 | c.2427C>G | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
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 |
ndh | 2101996 | c.1047C>T | synonymous_variant | 1.0 | ethionamide | |
delamanid | ||||||
isoniazid | ||||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.98 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
folC | 2747650 | c.-52G>A | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3840514 | p.Arg303Cys | missense_variant | 1.0 | cycloserine | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |