Run ID: ERR11252512
Sample name:
Date: 2024-05-22T08:49:55.650943
Number of reads: 3155721
Percentage reads mapped: 99.75
Median coverage: 97.0
Strain: lineage1.2.2.2;lineage4.3.4.2.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.9 |
lineage1.2.2 | Indo-Oceanic | RD239 | 0.09 |
lineage1.2.2.2 | Indo-Oceanic | RD239 | 0.1 |
lineage4 | Euro-American | None | 0.92 |
lineage4.3.4.2.1 | Euro-American (LAM) | RD174 | 0.91 |
lineage1 | Indo-Oceanic | RD239 | 0.05 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 0.89 |
lineage4.3.4.2 | Euro-American (LAM) | RD174 | 0.92 |
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 | 5075 | c.-165C>T | upstream_gene_variant | 0.17 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6112 | p.Met291Ile | missense_variant | 0.17 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrB | 6140 | p.Val301Leu | missense_variant | 0.85 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrB | 6745 | c.1506T>C | synonymous_variant | 0.18 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
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 | |||||
rpoC | 763552 | c.183C>T | synonymous_variant | 0.15 | rifampicin | Not assoc w R |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.93 | 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 |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 0.12 | linezolid | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.14 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embR | 1417491 | c.-144C>T | upstream_gene_variant | 0.91 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
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 |
ndh | 2102240 | p.Arg268His | missense_variant | 0.14 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Not assoc w R - Interim | |||||
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.11 | pyrazinamide | Not assoc w R |
Rv1979c | 2222098 | p.Thr356Lys | missense_variant | 0.14 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.16 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.12 | isoniazid | |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.86 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612009 | p.Ala370Thr | missense_variant | 0.92 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3840719 | c.702A>G | synonymous_variant | 0.86 | cycloserine | |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.95 | pyrazinamide | Not assoc w R |
clpC1 | 4040719 | c.-15A>G | upstream_gene_variant | 0.12 | pyrazinamide | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245670 | p.Ala813Gly | missense_variant | 0.1 | ethambutol | Not assoc w R - Interim |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.13 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.1 | ethambutol | Not assoc w R |
ethA | 4326148 | c.1326G>T | synonymous_variant | 0.19 | ethionamide | Not assoc w R - Interim |
ethA | 4326298 | c.1176G>T | synonymous_variant | 0.89 | ethionamide | |
ethA | 4326433 | c.1041G>A | synonymous_variant | 0.14 | ethionamide | |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.13 | ethionamide | Uncertain significance |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.16 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4408156 | p.Leu16Arg | missense_variant | 0.91 | streptomycin | Not assoc w R |