Run ID: ERR1213875
Sample name:
Date: 2024-04-15T11:15:25.795278
Number of reads: 8178800
Percentage reads mapped: 98.22
Median coverage: 22.0
Strain: lineage4.3.3
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.98 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.3 | Euro-American (LAM) | RD115 | 0.92 |
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 |
---|---|---|---|---|---|---|
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 | 8040 | p.Gly247Ser | missense_variant | 0.92 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rpoB | 762841 | p.Pro1012Leu | missense_variant | 1.0 | rifampicin | |
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
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 | 1471969 | n.124T>C | non_coding_transcript_exon_variant | 0.81 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472035 | n.190G>T | non_coding_transcript_exon_variant | 0.76 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472042 | n.197T>C | non_coding_transcript_exon_variant | 0.74 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472053 | n.211_212delGC | non_coding_transcript_exon_variant | 0.74 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472061 | n.216A>T | non_coding_transcript_exon_variant | 0.73 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472075 | n.230A>G | non_coding_transcript_exon_variant | 0.78 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.74 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473123 | n.1278A>T | non_coding_transcript_exon_variant | 0.85 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1473752 | n.95G>T | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
linezolid | ||||||
rrl | 1473806 | n.149C>T | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473815 | n.158T>C | non_coding_transcript_exon_variant | 0.99 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473836 | n.179A>G | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | Uncertain significance | |||||
rrl | 1473876 | n.219G>A | non_coding_transcript_exon_variant | 0.91 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473877 | n.220G>A | non_coding_transcript_exon_variant | 0.92 | capreomycin | |
linezolid | ||||||
rrl | 1473898 | n.241C>T | non_coding_transcript_exon_variant | 0.92 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1473923 | n.266C>A | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
linezolid | Uncertain significance | |||||
rrl | 1473924 | n.267_268insT | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
linezolid | ||||||
rrl | 1473943 | n.286G>T | non_coding_transcript_exon_variant | 0.94 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1473944 | n.287G>T | non_coding_transcript_exon_variant | 0.92 | capreomycin | |
linezolid | ||||||
rrl | 1473981 | n.324delGinsAT | non_coding_transcript_exon_variant | 0.84 | capreomycin | |
linezolid | ||||||
rrl | 1473995 | n.338G>T | non_coding_transcript_exon_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.91 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rrl | 1474028 | n.371T>C | non_coding_transcript_exon_variant | 0.83 | capreomycin | |
linezolid | ||||||
rrl | 1474029 | n.372G>A | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
linezolid | ||||||
rrl | 1474034 | n.377G>A | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
linezolid | ||||||
rrl | 1474040 | n.383G>A | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
linezolid | ||||||
rrl | 1474083 | n.426C>T | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1474111 | n.454T>C | non_coding_transcript_exon_variant | 0.89 | capreomycin | |
linezolid | ||||||
rrl | 1474140 | n.483C>T | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474151 | n.494C>T | non_coding_transcript_exon_variant | 0.96 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474181 | n.524C>A | non_coding_transcript_exon_variant | 0.95 | capreomycin | |
linezolid | ||||||
rrl | 1474266 | n.609T>C | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474291 | n.634_649delTTTCCTCTCCGGAGGAinsC | non_coding_transcript_exon_variant | 0.83 | capreomycin | |
linezolid | ||||||
rrl | 1474308 | n.651G>T | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474310 | n.653T>G | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1474362 | n.705A>G | non_coding_transcript_exon_variant | 0.76 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474374 | n.717T>A | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
linezolid | ||||||
rrl | 1474447 | n.790G>A | non_coding_transcript_exon_variant | 0.6 | capreomycin | |
linezolid | ||||||
rrl | 1474632 | n.975G>T | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 0.84 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474716 | n.1059A>G | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1474760 | n.1103A>G | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474794 | n.1137C>A | non_coding_transcript_exon_variant | 0.94 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474812 | n.1155G>A | non_coding_transcript_exon_variant | 0.99 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1474831 | n.1174A>G | non_coding_transcript_exon_variant | 0.99 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475005 | n.1348C>T | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
linezolid | ||||||
rrl | 1475006 | n.1349A>G | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
linezolid | ||||||
rrl | 1475013 | n.1356G>A | non_coding_transcript_exon_variant | 0.83 | capreomycin | |
linezolid | ||||||
rrl | 1475028 | n.1371G>A | non_coding_transcript_exon_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1475061 | n.1404C>T | non_coding_transcript_exon_variant | 0.93 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475202 | n.1545G>C | non_coding_transcript_exon_variant | 0.76 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475213 | n.1556C>T | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475252 | n.1595C>T | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
linezolid | ||||||
rrl | 1475266 | n.1609T>C | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475276 | n.1619T>C | non_coding_transcript_exon_variant | 0.68 | capreomycin | |
linezolid | ||||||
rrl | 1475289 | n.1632G>A | non_coding_transcript_exon_variant | 0.69 | capreomycin | |
linezolid | ||||||
rrl | 1475291 | n.1634A>C | non_coding_transcript_exon_variant | 0.69 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475297 | n.1640C>T | non_coding_transcript_exon_variant | 0.74 | capreomycin | |
linezolid | ||||||
rrl | 1475315 | n.1658A>C | non_coding_transcript_exon_variant | 0.71 | capreomycin | |
linezolid | ||||||
rrl | 1475333 | n.1676T>C | non_coding_transcript_exon_variant | 0.73 | capreomycin | |
linezolid | ||||||
rrl | 1475355 | n.1698C>T | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475369 | n.1712G>C | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
linezolid | ||||||
rrl | 1475402 | n.1745C>T | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1475419 | n.1762C>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475429 | n.1772G>A | non_coding_transcript_exon_variant | 0.85 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475446 | n.1789G>C | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
linezolid | ||||||
rrl | 1475505 | n.1848G>A | non_coding_transcript_exon_variant | 0.76 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.65 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475608 | n.1951T>C | non_coding_transcript_exon_variant | 0.56 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475638 | n.1981C>T | non_coding_transcript_exon_variant | 0.59 | capreomycin | |
linezolid | ||||||
rrl | 1475657 | n.2000A>G | non_coding_transcript_exon_variant | 0.64 | capreomycin | |
linezolid | ||||||
rrl | 1475881 | n.2224T>C | non_coding_transcript_exon_variant | 0.44 | capreomycin | |
linezolid | ||||||
rrl | 1475988 | n.2331A>G | non_coding_transcript_exon_variant | 0.52 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1475997 | n.2340A>T | non_coding_transcript_exon_variant | 0.52 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476086 | n.2429G>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476089 | n.2432T>C | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
linezolid | ||||||
rrl | 1476095 | n.2438C>G | non_coding_transcript_exon_variant | 0.66 | capreomycin | |
linezolid | ||||||
rrl | 1476115 | n.2458T>C | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476117 | n.2460G>C | non_coding_transcript_exon_variant | 0.69 | capreomycin | |
linezolid | ||||||
rrl | 1476214 | n.2557G>A | non_coding_transcript_exon_variant | 0.74 | capreomycin | |
linezolid | ||||||
rrl | 1476224 | n.2567A>G | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.75 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476281 | n.2624T>C | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476299 | n.2642C>T | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476583 | n.2926G>A | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476597 | n.2940G>A | non_coding_transcript_exon_variant | 0.71 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476628 | n.2971T>A | non_coding_transcript_exon_variant | 0.82 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476629 | n.2972C>A | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476716 | n.3059A>C | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476726 | n.3069A>G | non_coding_transcript_exon_variant | 0.68 | capreomycin | |
linezolid | ||||||
rrl | 1476746 | n.3089T>A | non_coding_transcript_exon_variant | 0.52 | capreomycin | |
linezolid | ||||||
rrl | 1476755 | n.3098G>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | |
linezolid | ||||||
rrl | 1476759 | n.3102T>A | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
linezolid | ||||||
rpsA | 1834836 | p.Met432Thr | missense_variant | 0.92 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.94 | linezolid | Not assoc w R |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 0.97 | isoniazid | 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 | 2746340 | p.Ala420Val | missense_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.94 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.95 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
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 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |