Run ID: SRR13861225
Sample name:
Date: 2024-10-03T16:15:01.699571
Number of reads: 466271
Percentage reads mapped: 46.67
Median coverage: 16.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
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 | ||||
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 | 715 | p.Thr239Pro | missense_variant | 1.0 | isoniazid | |
fgd1 | 490955 | p.Met58Arg | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
mshA | 574818 | c.-530G>C | upstream_gene_variant | 1.0 | isoniazid | |
ethionamide | ||||||
hadA | 731861 | c.-69G>C | upstream_gene_variant | 1.0 | isoniazid | |
rpsL | 781155 | c.-405G>A | upstream_gene_variant | 1.0 | streptomycin | |
fbiC | 1304529 | c.1599T>C | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
rrs | 1472614 | n.769G>T | non_coding_transcript_exon_variant | 0.45 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.43 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472655 | n.810G>A | non_coding_transcript_exon_variant | 0.42 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
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 | 0.58 | 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 | 0.64 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.53 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.64 | 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 | 0.65 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.55 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.67 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.69 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.56 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.45 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.36 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476517 | n.2860C>T | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476524 | n.2867C>A | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476572 | n.2915G>A | non_coding_transcript_exon_variant | 0.35 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476573 | n.2916A>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | Uncertain significance |
linezolid | ||||||
inhA | 1674607 | p.Pro136Ser | missense_variant | 1.0 | isoniazid | |
ethionamide | ||||||
inhA | 1674778 | p.Pro193Ala | missense_variant | 1.0 | isoniazid | |
ethionamide | ||||||
rpsA | 1833269 | c.-273G>T | upstream_gene_variant | 1.0 | pyrazinamide | |
bacA | 2064115 | p.Ala205Asp | missense_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
PPE35 | 2169081 | p.Leu511Ser | missense_variant | 1.0 | pyrazinamide | |
PPE35 | 2169202 | p.Ser471Pro | missense_variant | 1.0 | pyrazinamide | |
Rv1979c | 2222091 | c.1074G>T | synonymous_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2223306 | c.-142T>A | upstream_gene_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
pncA | 2289228 | p.Ile5Asn | missense_variant | 1.0 | pyrazinamide | |
kasA | 2518176 | p.Ala21Gly | missense_variant | 1.0 | isoniazid | |
eis | 2714755 | p.Pro193Gln | missense_variant | 1.0 | kanamycin | |
amikacin | ||||||
ahpC | 2726324 | c.132A>G | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
ahpC | 2726362 | p.Phe57Ser | missense_variant | 1.0 | isoniazid | |
pepQ | 2859580 | p.Leu280Arg | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
pepQ | 2859999 | c.420G>T | synonymous_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv2681 | 2997338 | c.600G>C | synonymous_variant | 1.0 | capreomycin | |
thyX | 3067940 | c.6C>G | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3074620 | c.-149C>A | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
mtrB | 3626051 | p.Ser188Trp | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
ddn | 3986889 | p.Phe16Val | missense_variant | 1.0 | pretomanid | |
delamanid | ||||||
embA | 4244723 | p.Gln497His | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4267979 | c.858G>C | synonymous_variant | 1.0 | ethambutol |