Run ID: SRR10809102
Sample name:
Date: 2024-04-16T10:28:54.040199
Number of reads: 2957921
Percentage reads mapped: 99.57
Median coverage: 96.0
Strain: lineage4.6.5
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6.5 | Euro-American | None | 1.0 |
lineage4.6 | Euro-American | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Trp191Arg | Uncertain significance | Mutation from literature | |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | tlyA | p.Asn236Lys | Assoc w R | |
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
tlyA | 1918647 | p.Asn236Lys | missense_variant | 1.0 | capreomycin | Assoc w R | |
katG | 2155541 | p.Trp191Arg | missense_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1186 | p.Glu396Lys | missense_variant | 1.0 | isoniazid | Uncertain significance |
dnaA | 1326 | p.Gln442His | missense_variant | 1.0 | isoniazid | Uncertain significance |
gyrB | 5489 | p.Ile84Val | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | 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 | |||||
fgd1 | 490756 | c.-27T>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
rpoB | 761550 | p.Ser582Ala | missense_variant | 0.68 | rifampicin | Uncertain significance |
rpoB | 761593 | p.Ala596Gly | missense_variant | 0.2 | rifampicin | Uncertain significance |
rpoC | 763193 | c.-177C>T | upstream_gene_variant | 1.0 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 777974 | c.507C>T | synonymous_variant | 1.0 | clofazimine | Not assoc w R - Interim |
bedaquiline | 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 | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1471670 | n.-176G>A | 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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
folC | 2746764 | p.Leu279Val | missense_variant | 1.0 | para-aminosalicylic_acid | |
folC | 2746995 | p.Val202Ile | missense_variant | 1.0 | para-aminosalicylic_acid | |
ribD | 2987039 | c.201C>T | synonymous_variant | 1.0 | para-aminosalicylic_acid | |
alr | 3841546 | c.-126C>A | upstream_gene_variant | 0.13 | cycloserine | |
clpC1 | 4038332 | c.2373C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | 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 |