Run ID: ERR4799172
Sample name:
Date: 2024-03-26T16:02:14.113800
Number of reads: 3168331
Percentage reads mapped: 99.68
Median coverage: 93.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.98 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.His1002Arg | Uncertain significance | Mutation from literature |
pyrazinamide | pncA | c.391dupG | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94His | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94His | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.655dupG | Assoc w R | |
c.550_551dupGG | Assoc w R | |||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7581 | p.Asp94His | missense_variant | 0.99 | moxifloxacin | Assoc w R | High-level resistance |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288850 | c.391dupG | frameshift_variant | 0.98 | pyrazinamide | Assoc w R | |
embB | 4249518 | p.His1002Arg | missense_variant | 0.96 | ethambutol | Uncertain significance | Mutation from literature |
ethA | 4326818 | c.655dupG | frameshift_variant | 0.12 | ethionamide | Assoc w R | |
ethA | 4326922 | c.550_551dupGG | frameshift_variant | 0.8 | ethionamide | 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 | |||||
rpoC | 764669 | p.Pro434Thr | missense_variant | 0.85 | rifampicin | Uncertain significance |
rpoC | 764817 | p.Val483Ala | missense_variant | 0.1 | rifampicin | 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 | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472753 | n.908A>C | non_coding_transcript_exon_variant | 0.98 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2223491 | c.-327C>A | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Uncertain significance | |||||
pncA | 2289969 | c.-728G>C | upstream_gene_variant | 1.0 | pyrazinamide | |
ald | 3087647 | c.830dupG | frameshift_variant | 1.0 | cycloserine | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.98 | ethionamide | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247028 | p.Leu172Arg | missense_variant | 0.17 | ethambutol | |
ubiA | 4269124 | p.Ala237Val | missense_variant | 0.97 | ethambutol | Uncertain significance |
ethA | 4326844 | c.630C>G | synonymous_variant | 0.99 | ethionamide | Not assoc w R - Interim |
whiB6 | 4338362 | p.Arg54Gly | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | 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 | |||||
gid | 4408061 | p.His48Asn | missense_variant | 0.99 | streptomycin | Uncertain significance |