Run ID: SRR29273723
Sample name:
Date: 2024-10-04T04:52:51.837868
Number of reads: 3028638
Percentage reads mapped: 99.55
Median coverage: 90.0
Strain: lineage4.1.2
Spoligotype:
Drug-resistance: RR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 1.0 |
lineage4.1.2 | Euro-American | None | 0.99 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Tyr | Assoc w R | |
p.Ser441Ala | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB | ||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | pncA | p.Val139Met | Assoc w R | |
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 |
---|---|---|---|---|---|---|---|
rpoB | 761109 | p.Asp435Tyr | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpoB | 761127 | p.Ser441Ala | missense_variant | 1.0 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
pncA | 2288827 | p.Val139Met | missense_variant | 1.0 | pyrazinamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 166 | p.Ile56Val | missense_variant | 0.99 | isoniazid | Uncertain significance |
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 | |||||
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1253131 | c.1404G>A | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
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 |
katG | 2154796 | p.Gln439Pro | missense_variant | 1.0 | isoniazid | Uncertain significance |
katG | 2156360 | c.-249T>G | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
ahpC | 2726142 | c.-51G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
folC | 2747022 | p.Val193Ile | missense_variant | 1.0 | para-aminosalicylic_acid | |
ribD | 2987427 | p.Thr197Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
Rv2752c | 3065081 | p.His371Tyr | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448656 | c.153G>A | synonymous_variant | 1.0 | ethionamide | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
fbiA | 3641164 | p.Ile208Val | missense_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
glpK | 4139261 | c.495C>G | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | ||||||
isoniazid | Not assoc w R - Interim | |||||
streptomycin | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
ethambutol | Not assoc w R - Interim | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | 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 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin |