Run ID: ERR025437
Sample name:
Date: 2024-10-05T11:04:00.315163
Number of reads: 754225
Percentage reads mapped: 99.27
Median coverage: 16.0
Strain: lineage1.2.1.2.1;lineage2.2.2;lineage4.1.2;lineage4.2.2
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2.2 | Euro-American (Ural) | None | 0.06 |
lineage1.2.1.2 | Indo-Oceanic | RD239 | 0.65 |
lineage2 | East-Asian | RD105 | 0.06 |
lineage4.1.2 | Euro-American | None | 0.1 |
lineage2.2.2 | East-Asian (Beijing) | RD105;RD207 | 0.05 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.08 |
lineage4 | Euro-American | None | 0.29 |
lineage1 | Indo-Oceanic | RD239 | 0.64 |
lineage1.2.1.2.1 | Indo-Oceanic | RD239 | 0.62 |
lineage1.2.1 | Indo-Oceanic | RD239 | 0.59 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.1343delA | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
ethA | 4326130 | c.1343delA | frameshift_variant | 0.36 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1302 | c.1302C>A | synonymous_variant | 0.48 | isoniazid | Not assoc w R |
gyrB | 6112 | p.Met291Ile | missense_variant | 0.74 | 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 | 9260 | c.1959G>C | synonymous_variant | 0.71 | 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 | |||||
Rv0010c | 13175 | c.384T>C | synonymous_variant | 0.67 | isoniazid | Not assoc w R |
Rv0010c | 13298 | p.Ile87Met | missense_variant | 0.57 | isoniazid | Not assoc w R |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.78 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.58 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.64 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.78 | rifampicin | Not assoc w R |
rpoC | 763531 | c.162G>C | synonymous_variant | 0.65 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.8 | rifampicin | Not assoc w R |
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.88 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpS5 | 778743 | p.Val55Met | missense_variant | 0.36 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 0.52 | linezolid | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.68 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.75 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.62 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | 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 | 2062922 | p.Ile603Val | missense_variant | 0.62 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.78 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.83 | pyrazinamide | Not assoc w R |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.58 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.37 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.57 | isoniazid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
fbiD | 3339417 | c.300A>G | synonymous_variant | 0.58 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.59 | ethionamide | Uncertain significance |
whiB7 | 3568488 | c.191delG | frameshift_variant | 0.68 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.61 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.76 | pyrazinamide | Not assoc w R - Interim |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.71 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243580 | c.348G>A | synonymous_variant | 0.62 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.59 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.65 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.69 | ethambutol | Not assoc w R |
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 | 4338603 | c.-82C>T | upstream_gene_variant | 0.58 | 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 | ||||||
gid | 4407873 | c.330G>T | synonymous_variant | 0.82 | streptomycin | Not assoc w R |