Run ID: SRR6044890
Sample name:
Date: 2024-04-15T08:12:12.158621
Number of reads: 62968
Percentage reads mapped: 21.51
Median coverage: 0.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 0.98 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.98 |
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 |
---|---|---|---|---|---|---|
ccsA | 620367 | c.477T>C | synonymous_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
ccsA | 620373 | c.483C>G | synonymous_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
rpoC | 766765 | c.3396A>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 766774 | c.3405T>C | synonymous_variant | 1.0 | rifampicin | |
rpoC | 767098 | c.3729T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rpoC | 767119 | c.3750A>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R - Interim |
rplC | 801276 | c.468G>C | synonymous_variant | 0.91 | linezolid | |
lpqB | 3624125 | c.786A>G | synonymous_variant | 1.0 | bedaquiline | |
rifampicin | ||||||
ddn | 3986627 | c.-217C>T | upstream_gene_variant | 1.0 | delamanid | |
pretomanid | ||||||
ddn | 3986648 | c.-196C>G | upstream_gene_variant | 1.0 | delamanid | |
pretomanid | ||||||
ddn | 3986654 | c.-190C>A | upstream_gene_variant | 1.0 | delamanid | |
pretomanid | ||||||
clpC1 | 4038314 | c.2391T>A | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4038347 | c.2358G>C | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4040336 | c.369G>T | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4040354 | c.351A>G | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4040363 | c.342A>T | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4040380 | c.325T>C | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4040381 | c.324T>C | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4040387 | c.318A>G | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4040393 | c.312G>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040522 | c.183T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040528 | c.177G>T | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4040531 | c.174T>C | synonymous_variant | 1.0 | pyrazinamide | |
clpC1 | 4040534 | c.171A>G | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040551 | c.154T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
embB | 4248133 | c.1620C>A | synonymous_variant | 1.0 | ethambutol | |
embB | 4248143 | c.1630_1632delTTGinsCC | frameshift_variant&missense_variant | 1.0 | ethambutol | |
embB | 4248157 | c.1644A>C | synonymous_variant | 1.0 | ethambutol |