Run ID: DRR184902
Sample name:
Date: 2024-04-15T23:26:52.891830
Number of reads: 1516946
Percentage reads mapped: 91.18
Median coverage: 61.0
Strain: lineage2.2.1;lineage4.8
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.08 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.07 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.1 |
lineage4 | Euro-American | None | 0.95 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.87 |
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 | 371 | p.Pro124Leu | missense_variant | 0.87 | isoniazid | Not assoc w R |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.13 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.15 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.15 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.13 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1258c | 1406789 | c.552C>T | synonymous_variant | 0.91 | streptomycin | Not assoc w R - Interim |
isoniazid | Not assoc w R - Interim | |||||
pyrazinamide | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.93 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rrl | 1476225 | n.2568T>G | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476229 | n.2572C>G | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476251 | n.2594T>G | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476256 | n.2599A>G | non_coding_transcript_exon_variant | 0.26 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.28 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476297 | n.2640C>A | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476353 | n.2696G>A | non_coding_transcript_exon_variant | 0.27 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>T | non_coding_transcript_exon_variant | 0.28 | capreomycin | |
linezolid | ||||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.27 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.18 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.2 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476470 | n.2813C>T | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.21 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.19 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476513 | n.2856G>A | non_coding_transcript_exon_variant | 0.14 | capreomycin | |
linezolid | ||||||
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.17 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.16 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476528 | n.2871A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476544 | n.2887T>C | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476545 | n.2888C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | |
linezolid | ||||||
rrl | 1476566 | n.2909A>G | non_coding_transcript_exon_variant | 0.1 | capreomycin | |
linezolid | ||||||
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
inhA | 1673868 | c.-334C>G | upstream_gene_variant | 0.85 | ethionamide | |
isoniazid | Uncertain significance | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.13 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.12 | 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 | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.13 | cycloserine | |
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.16 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3840764 | c.657G>C | synonymous_variant | 0.91 | cycloserine | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | 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 | |||||
gid | 4407927 | p.Glu92Asp | missense_variant | 0.11 | streptomycin | Not assoc w R |