Run ID: SRR3732704
Sample name:
Date: 2024-10-04T13:37:59.147428
Number of reads: 4170259
Percentage reads mapped: 99.59
Median coverage: 81.0
Strain: lineage4.1.2.1;lineage4.6.2.2
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6 | Euro-American | None | 0.66 |
lineage4.6.2 | Euro-American | RD726 | 0.58 |
lineage4.1 | Euro-American | None | 0.4 |
lineage4.6.2.2 | Euro-American (Cameroon) | RD726 | 0.58 |
lineage4.1.2 | Euro-American | None | 0.42 |
lineage4.1.2.1 | Euro-American (Haarlem) | RD182 | 0.47 |
lineage4 | Euro-American | 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 |
---|---|---|---|---|---|---|
gyrA | 7361 | c.60C>T | synonymous_variant | 0.39 | levofloxacin | |
moxifloxacin | ||||||
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 | |||||
fgd1 | 491591 | p.Lys270Met | missense_variant | 0.46 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Not assoc w R | |||||
mshA | 575679 | p.Asn111Ser | missense_variant | 0.43 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.28 | ethionamide | Uncertain significance |
rpoB | 760115 | c.309C>T | synonymous_variant | 0.33 | 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 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 778298 | c.183G>A | synonymous_variant | 0.59 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 0.99 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
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 |
bacA | 2063187 | c.1542C>T | synonymous_variant | 0.66 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
PPE35 | 2168569 | p.Thr682Pro | missense_variant | 0.44 | pyrazinamide | |
Rv1979c | 2221746 | c.1416_1418dupCCG | disruptive_inframe_insertion | 0.5 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2518076 | c.-39C>T | upstream_gene_variant | 0.33 | isoniazid | |
Rv2680 | 2996208 | p.Ala35Asp | missense_variant | 0.59 | capreomycin | Uncertain significance |
thyX | 3067474 | p.Pro158Ala | missense_variant | 0.55 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.4 | cycloserine | |
Rv3083 | 3448567 | p.His22Asp | missense_variant | 0.7 | ethionamide | Uncertain significance |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.35 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626161 | c.453C>T | synonymous_variant | 0.41 | rifampicin | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
mtrA | 3627756 | c.-407A>T | upstream_gene_variant | 0.49 | rifampicin | |
bedaquiline | ||||||
clpC1 | 4038408 | p.Pro766Leu | missense_variant | 0.43 | pyrazinamide | Uncertain significance |
clpC1 | 4038857 | c.1848C>A | synonymous_variant | 0.29 | pyrazinamide | |
embC | 4239298 | c.-565C>T | upstream_gene_variant | 0.48 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.31 | ethambutol | Not assoc w R |
aftB | 4267272 | p.Lys522Arg | missense_variant | 0.59 | ethambutol | Not assoc w R |
ethA | 4326739 | c.735C>G | synonymous_variant | 0.62 | ethionamide | Not assoc w R - Interim |
ethR | 4328004 | c.456G>A | synonymous_variant | 0.62 | ethionamide | Not assoc w R - Interim |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin |