Run ID: SRR13861677
Sample name:
Date: 2024-10-04T22:11:41.197681
Number of reads: 368296
Percentage reads mapped: 36.86
Median coverage: 12.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Gly234Glu | Uncertain significance | Mutation from literature |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.888G>A | Uncertain significance | Mutation from literature |
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 |
---|---|---|---|---|---|---|---|
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.46 | streptomycin | Uncertain significance | Mutation from literature |
katG | 2155411 | p.Gly234Glu | missense_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
Rv0010c | 13524 | p.Gly12Ala | missense_variant | 1.0 | isoniazid | |
ccsA | 620690 | p.Val267Glu | missense_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
mmaA3 | 738209 | c.-60A>T | upstream_gene_variant | 1.0 | isoniazid | |
rpoB | 761961 | p.Pro719Thr | missense_variant | 1.0 | rifampicin | |
rpoC | 764895 | p.Ile509Thr | missense_variant | 1.0 | rifampicin | |
mmpL5 | 777574 | p.Phe303Leu | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 777578 | c.903C>G | synonymous_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
mmpL5 | 778982 | c.-502A>C | upstream_gene_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
rplC | 801169 | p.Lys121* | stop_gained | 1.0 | linezolid | |
rrs | 1472614 | n.769G>T | non_coding_transcript_exon_variant | 0.6 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.58 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.54 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472658 | n.813G>A | non_coding_transcript_exon_variant | 0.46 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472661 | n.816A>G | non_coding_transcript_exon_variant | 0.46 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472665 | n.820G>A | non_coding_transcript_exon_variant | 0.46 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472669 | n.824_825insTAGG | non_coding_transcript_exon_variant | 0.52 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472678 | n.833_834delTTinsGCC | non_coding_transcript_exon_variant | 0.5 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472684 | n.839_845delGGGATCCinsA | non_coding_transcript_exon_variant | 0.5 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472695 | n.850C>T | non_coding_transcript_exon_variant | 0.5 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472697 | n.852T>C | non_coding_transcript_exon_variant | 0.48 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.5 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.52 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.48 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.48 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrl | 1474052 | n.395G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.5 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.65 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.65 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.7 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.46 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.61 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.56 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.59 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476479 | n.2822T>G | non_coding_transcript_exon_variant | 0.5 | capreomycin | |
linezolid | ||||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.5 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
tlyA | 1918432 | p.Pro165Thr | missense_variant | 1.0 | capreomycin | |
ndh | 2101769 | p.Arg425His | missense_variant | 1.0 | isoniazid | Uncertain significance |
delamanid | ||||||
ethionamide | ||||||
katG | 2155508 | p.Ala202Ser | missense_variant | 1.0 | isoniazid | Uncertain significance |
pncA | 2289474 | c.-233C>G | upstream_gene_variant | 1.0 | pyrazinamide | |
folC | 2746862 | p.Leu246Arg | missense_variant | 1.0 | para-aminosalicylic_acid | |
folC | 2747268 | p.Asp111His | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv2752c | 3065109 | c.1083A>G | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
ethambutol | ||||||
lpqB | 3624508 | p.Ile135Val | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
mtrB | 3625247 | p.Arg456Pro | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
clpC1 | 4038468 | p.Asp746Gly | missense_variant | 1.0 | pyrazinamide | |
clpC1 | 4040148 | p.Lys186Ile | missense_variant | 1.0 | pyrazinamide | |
ethR | 4327643 | p.Thr32Ile | missense_variant | 1.0 | ethionamide |