Run ID: SRR13837876
Sample name:
Date: 2024-10-04T19:30:55.235391
Number of reads: 1470894
Percentage reads mapped: 98.12
Median coverage: 49.0
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 |
---|---|---|---|---|---|---|
gyrB | 6624 | p.Ser462* | stop_gained | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | ||||||
gyrA | 7285 | c.-17T>C | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 8798 | c.1497C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
mmaA3 | 737872 | p.Asp93Ala | missense_variant | 1.0 | isoniazid | |
mmaA3 | 738202 | c.-53A>C | upstream_gene_variant | 1.0 | isoniazid | |
rpoC | 764438 | c.1069_1070insA | frameshift_variant | 1.0 | rifampicin | |
mmpL5 | 775795 | p.Ala896Ser | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
fbiC | 1303593 | c.663G>A | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
embR | 1416428 | c.919_920insT | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
rrs | 1471798 | n.-48G>A | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472913 | n.1068G>C | non_coding_transcript_exon_variant | 0.98 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1476167 | n.2510T>A | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | ||||||
inhA | 1674226 | p.Arg9Trp | missense_variant | 0.98 | isoniazid | |
ethionamide | ||||||
rpsA | 1833352 | c.-190C>A | upstream_gene_variant | 1.0 | pyrazinamide | |
rpsA | 1833710 | p.Tyr57Asp | missense_variant | 1.0 | pyrazinamide | |
rpsA | 1834711 | c.1170C>T | synonymous_variant | 0.98 | pyrazinamide | |
ndh | 2102326 | c.717G>T | synonymous_variant | 1.0 | isoniazid | |
delamanid | ||||||
ethionamide | ||||||
Rv1979c | 2222739 | c.426C>A | synonymous_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2222936 | p.Ala77Thr | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
eis | 2714217 | c.1115dupC | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
eis | 2714361 | c.972C>A | synonymous_variant | 1.0 | kanamycin | |
amikacin | ||||||
ahpC | 2725906 | c.-287C>G | upstream_gene_variant | 1.0 | isoniazid | |
Rv2477c | 2782975 | c.1068C>T | synonymous_variant | 1.0 | kanamycin | Not assoc w R - Interim |
levofloxacin | Not assoc w R - Interim | |||||
moxifloxacin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
ethambutol | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
pepQ | 2859813 | p.Ile202Met | missense_variant | 1.0 | bedaquiline | |
clofazimine | ||||||
pepQ | 2860286 | p.Val45Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
ribD | 2987503 | p.Gly222Val | missense_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3087394 | p.Ala192Val | missense_variant | 1.0 | cycloserine | |
ald | 3087464 | c.645C>T | synonymous_variant | 1.0 | cycloserine | |
ald | 3087512 | c.693T>A | synonymous_variant | 1.0 | cycloserine | |
Rv3083 | 3448303 | c.-201G>C | upstream_gene_variant | 1.0 | ethionamide | |
lpqB | 3623311 | p.Pro534Ser | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
lpqB | 3623400 | p.Val504Glu | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
lpqB | 3624438 | p.Gln158Leu | missense_variant | 1.0 | rifampicin | |
bedaquiline | ||||||
rpoA | 3879111 | c.-604G>C | upstream_gene_variant | 1.0 | rifampicin | |
embC | 4241874 | p.Leu671Arg | missense_variant | 1.0 | ethambutol | |
embC | 4242816 | p.Trp985* | stop_gained | 0.98 | ethambutol | |
embB | 4248365 | p.Val618Met | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4267893 | p.Ile315Ser | missense_variant | 1.0 | ethambutol | |
aftB | 4268516 | c.321A>G | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
ethR | 4326691 | c.-858C>A | upstream_gene_variant | 1.0 | ethionamide |