Run ID: SRR28393617
Sample name:
Date: 2024-05-22T08:04:52.446805
Number of reads: 6767533
Percentage reads mapped: 99.73
Median coverage: 183.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Trp | Assoc w R | |
isoniazid | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
p.Ser94Ala | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | ||
ethambutol | embB | p.Gly406Asp | Assoc w R | |
pyrazinamide | pncA | p.Tyr103Cys | Assoc w R | |
streptomycin | gid | c.102delG | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-12C>T | Assoc w R | |
cycloserine | ||||
ethionamide | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T |
p.Ser94Ala | Assoc w R - Interim | |||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Trp | missense_variant | 1.0 | rifampicin | Assoc w R | |
inhA | 1673423 | c.-779G>T | upstream_gene_variant | 1.0 | isoniazid | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethionamide | Assoc w R - Interim | Alias fabG1_c.-17G>T | |||||
inhA | 1674481 | p.Ser94Ala | missense_variant | 0.99 | isoniazid | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethionamide | Assoc w R - Interim | ||||||
pncA | 2288934 | p.Tyr103Cys | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 1.0 | kanamycin | Assoc w R | |
embB | 4247730 | p.Gly406Asp | missense_variant | 1.0 | ethambutol | Assoc w R | |
gid | 4408100 | c.102delG | frameshift_variant | 0.99 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 0.99 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
ccsA | 620475 | c.585G>A | synonymous_variant | 1.0 | capreomycin | Not assoc w R - Interim |
amikacin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
tlyA | 1918745 | c.806A>G | stop_lost&splice_region_variant | 1.0 | capreomycin | Uncertain significance |
katG | 2155025 | c.1075_1086delGCCGGTGCCGGC | conservative_inframe_deletion | 1.0 | isoniazid | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.99 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2289656 | c.-415C>A | upstream_gene_variant | 1.0 | pyrazinamide | |
folC | 2747612 | c.-14T>G | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3087095 | c.276C>T | synonymous_variant | 1.0 | cycloserine | |
glpK | 4138645 | p.Pro371Ser | missense_variant | 0.93 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | ||||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245899 | c.2667C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
ubiA | 4269302 | p.Leu178Val | missense_variant | 1.0 | ethambutol | 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 | 4338632 | c.-112_-111insTTAACAGG | upstream_gene_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance |