Run ID: ERR3324330
Sample name:
Date: 2024-10-04T03:32:49.671183
Number of reads: 2063393
Percentage reads mapped: 99.19
Median coverage: 90.0
Strain: lineage4.8;lineage5.1.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 0.92 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.85 |
lineage5.1.1 | West-Africa 1 | RD711 | 0.08 |
lineage5 | West-Africa 1 | RD711 | 0.1 |
lineage5.1 | West-Africa 1 | RD711 | 0.1 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 770 | p.Ala257Val | missense_variant | 0.88 | isoniazid | Uncertain significance |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.23 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.11 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.18 | isoniazid | Not assoc w R |
Rv0010c | 13579 | c.-21G>A | upstream_gene_variant | 0.2 | isoniazid | Uncertain significance |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.14 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
hadA | 731750 | c.-180G>C | upstream_gene_variant | 0.12 | isoniazid | |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.1 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.18 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1258c | 1406402 | c.939C>G | synonymous_variant | 0.88 | streptomycin | |
pyrazinamide | ||||||
isoniazid | ||||||
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.18 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.85 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
inhA | 1673338 | c.-864G>A | upstream_gene_variant | 0.13 | isoniazid | |
ethionamide | ||||||
tsnR | 1853565 | c.-41G>A | upstream_gene_variant | 0.17 | linezolid | Uncertain significance |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.2 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
ndh | 2101840 | c.1203G>A | synonymous_variant | 0.17 | isoniazid | Not assoc w R - Interim |
delamanid | Not assoc w R - Interim | |||||
ethionamide | Not assoc w R - Interim | |||||
ndh | 2101921 | c.1122G>A | synonymous_variant | 0.25 | isoniazid | Not assoc w R - Interim |
delamanid | Not assoc w R - Interim | |||||
ethionamide | Not assoc w R - Interim | |||||
ndh | 2103112 | c.-70G>T | upstream_gene_variant | 0.15 | isoniazid | Not assoc w R - Interim |
delamanid | Uncertain significance | |||||
ethionamide | Uncertain significance | |||||
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.18 | pyrazinamide | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.81 | pyrazinamide | 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 | |||||
pncA | 2290062 | c.-821G>A | upstream_gene_variant | 0.23 | pyrazinamide | |
Rv2477c | 2783769 | p.Gly92Arg | missense_variant | 0.87 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
amikacin | ||||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.87 | capreomycin | |
Rv3083 | 3449644 | p.Ala381Thr | missense_variant | 0.79 | ethionamide | Uncertain significance |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.34 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
alr | 3840932 | c.489C>T | synonymous_variant | 0.14 | cycloserine | |
ddn | 3986987 | c.144G>T | synonymous_variant | 0.16 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
ddn | 3987180 | p.Asp113Asn | missense_variant | 0.19 | pretomanid | |
delamanid | Uncertain significance | |||||
glpK | 4138377 | p.Val460Ala | missense_variant | 0.13 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
glpK | 4139131 | p.Glu209Lys | missense_variant | 0.15 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Uncertain significance | |||||
embC | 4239843 | c.-20A>C | upstream_gene_variant | 0.1 | ethambutol | Not assoc w R - Interim |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.18 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4244220 | c.988C>T | synonymous_variant | 0.14 | ethambutol | Not assoc w R |
aftB | 4268050 | p.Pro263Thr | missense_variant | 0.81 | ethambutol | |
ethA | 4326928 | c.546C>T | synonymous_variant | 0.18 | ethionamide | Not assoc w R - Interim |
ethA | 4327103 | p.Gly124Asp | missense_variant | 0.18 | ethionamide | Uncertain significance |
whiB6 | 4338547 | c.-26A>G | upstream_gene_variant | 0.12 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | 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 | 0.26 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407790 | p.Ala138Val | missense_variant | 0.8 | streptomycin | Uncertain significance |