Run ID: SRR1214871
Sample name:
Date: 2024-04-16T00:49:51.975450
Number of reads: 1956945
Percentage reads mapped: 96.48
Median coverage: 12.0
Strain: lineage4.1.2.1;lineage4.2.1;lineage4.9
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 0.15 |
lineage4.2 | Euro-American | None | 0.52 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.17 |
lineage4 | Euro-American | None | 1.0 |
lineage4.2.1 | Euro-American (TUR) | None | 0.41 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.64 |
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 |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rpoB | 760115 | c.309C>T | synonymous_variant | 0.3 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.4 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | 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 |
rrl | 1475145 | n.1488C>T | non_coding_transcript_exon_variant | 0.69 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.47 | isoniazid | |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.58 | ethambutol | Not assoc w R - Interim |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.75 | ethionamide | |
gid | 4408027 | p.Leu59Arg | missense_variant | 0.63 | streptomycin | Uncertain significance |