Run ID: SRR13861632
Sample name:
Date: 2024-10-04T00:30:42.359943
Number of reads: 472195
Percentage reads mapped: 9.45
Median coverage: 15.0
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 | ||||
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 |
---|---|---|---|---|---|---|---|
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 | ||||||
Rv0565c | 657622 | c.-152G>A | upstream_gene_variant | 1.0 | ethionamide | |
mmaA3 | 738209 | c.-60A>T | upstream_gene_variant | 1.0 | isoniazid | |
rpoB | 759805 | c.-2T>C | upstream_gene_variant | 1.0 | rifampicin | |
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 | ||||||
rrl | 1474052 | n.395G>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | |
linezolid | ||||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.81 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.85 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.84 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.84 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.86 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.83 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.83 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.83 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.84 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.86 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.87 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.87 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.86 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.86 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476479 | n.2822T>G | non_coding_transcript_exon_variant | 0.2 | capreomycin | |
linezolid | ||||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.55 | capreomycin | Not assoc w R |
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 | |
whiB7 | 3568816 | c.-137C>T | upstream_gene_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
whiB7 | 3569222 | c.-543G>A | upstream_gene_variant | 1.0 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
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 | |
embC | 4240125 | p.Cys88Tyr | missense_variant | 1.0 | ethambutol | |
ethR | 4327643 | p.Thr32Ile | missense_variant | 1.0 | ethionamide |