Run ID: ERR4799169
Sample name:
Date: 2024-04-16T04:53:40.844958
Number of reads: 3284280
Percentage reads mapped: 99.69
Median coverage: 88.0
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 | 0.99 |
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.Gln497Lys | Assoc w R | |
pyrazinamide | pncA | p.Val155Met | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Glu501Asp | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrB | p.Glu501Asp | Assoc w R - Interim | |
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 | 6742 | p.Glu501Asp | missense_variant | 1.0 | levofloxacin | Assoc w R - Interim | |
moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.96 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288779 | p.Val155Met | missense_variant | 0.99 | pyrazinamide | Assoc w R | |
embB | 4248002 | p.Gln497Lys | missense_variant | 1.0 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5332 | c.93C>T | synonymous_variant | 0.95 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8168 | p.Glu289Asp | missense_variant | 0.97 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
Rv0565c | 656265 | c.1204_1205delAC | frameshift_variant | 0.97 | ethionamide | Uncertain significance |
nusG | 734658 | c.405A>G | synonymous_variant | 0.99 | rifampicin | Not assoc w R |
rpoC | 766485 | p.Val1039Ala | missense_variant | 0.99 | 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 | ||||||
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 |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 1.0 | pyrazinamide | 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 | |||||
folC | 2747470 | p.Ile43Ala | missense_variant | 0.97 | para-aminosalicylic_acid | |
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.96 | capreomycin | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.97 | ethionamide | Uncertain significance |
Rv3236c | 3613636 | c.-520A>G | upstream_gene_variant | 0.96 | pyrazinamide | Not assoc w R |
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 0.97 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245417 | p.Gly729Arg | missense_variant | 0.99 | ethambutol | Uncertain significance |
ubiA | 4269298 | p.Ile179Thr | missense_variant | 0.98 | ethambutol | Uncertain significance |
ethA | 4327301 | p.Asp58Gly | missense_variant | 1.0 | ethionamide | 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 |