Run ID: SRR7069399
Sample name:
Date: 2024-05-20T09:25:38.658646
Number of reads: 1397829
Percentage reads mapped: 58.42
Median coverage: 43.0
Strain: lineage3
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.888G>A | Uncertain significance | Mutation from literature |
gid | c.115delC | Assoc w R | ||
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 |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | 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 | |||||
mmpL5 | 776100 | p.Thr794Ile | 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 |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
levofloxacin | Not assoc w R | |||||
sigE | 1364170 | c.-243C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
embR | 1416561 | p.Lys263Glu | missense_variant | 1.0 | ethambutol | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
capreomycin | ||||||
rrs | 1472517 | n.672T>A | non_coding_transcript_exon_variant | 0.44 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472518 | n.673G>T | non_coding_transcript_exon_variant | 0.47 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.6 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.6 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472544 | n.699C>A | non_coding_transcript_exon_variant | 0.58 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.52 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472566 | n.721G>A | non_coding_transcript_exon_variant | 0.5 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.58 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.65 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.65 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.5 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.92 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.82 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.78 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472677 | n.832C>T | non_coding_transcript_exon_variant | 0.72 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
capreomycin | ||||||
rrs | 1472690 | n.845C>A | non_coding_transcript_exon_variant | 0.8 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
capreomycin | ||||||
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.74 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.73 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.73 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.73 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.72 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.58 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.4 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.4 | kanamycin | Uncertain significance |
amikacin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
rrl | 1475943 | n.2286G>A | non_coding_transcript_exon_variant | 0.4 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475952 | n.2295A>G | non_coding_transcript_exon_variant | 0.43 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476250 | n.2593C>G | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476251 | n.2594T>C | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476257 | n.2600G>C | non_coding_transcript_exon_variant | 0.52 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.68 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476280 | n.2623A>C | non_coding_transcript_exon_variant | 0.59 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476293 | n.2636C>T | non_coding_transcript_exon_variant | 0.56 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476294 | n.2637A>G | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476295 | n.2638C>G | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476296 | n.2639C>T | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476297 | n.2640C>T | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476301 | n.2644A>T | non_coding_transcript_exon_variant | 0.63 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476302 | n.2645G>A | non_coding_transcript_exon_variant | 0.53 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476311 | n.2654G>C | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476312 | n.2655T>C | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476313 | n.2656G>A | non_coding_transcript_exon_variant | 0.56 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.77 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.81 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.84 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.85 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.85 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.21 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.8 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.89 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.84 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.67 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.61 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
tsnR | 1854066 | p.Ala154Val | missense_variant | 1.0 | linezolid | |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | 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 | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 1.0 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 1.0 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
ethambutol | Not assoc w R | |||||
levofloxacin | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
fbiA | 3641453 | p.Arg304Gln | missense_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
alr | 3841473 | c.-53G>A | upstream_gene_variant | 1.0 | cycloserine | |
panD | 4044872 | c.-591C>T | upstream_gene_variant | 1.0 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
ethambutol | Not assoc w R | |||||
levofloxacin | Not assoc w R | |||||
embC | 4241465 | p.Phe535Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
embC | 4242075 | p.Arg738Gln | missense_variant | 1.0 | ethambutol | Not assoc w R |
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 | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |