Run ID: bb44797c-ee27-473a-a09f-dfe3a6e0ff84
Sample name:
Date: 07-01-2023 05:11:56
Number of reads: 1886737
Percentage reads mapped: 99.09
Median coverage: 61
Strain: lineage4.1.1.3
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.1 | Euro-American | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | RD193 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Leu452Pro | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | |
ahpC | p.Asp73His | Uncertain significance | ||
ethambutol | ||||
pyrazinamide | pncA | p.Trp68* | Assoc w R - interim | |
moxifloxacin | ||||
levofloxacin | ||||
bedaquiline | ||||
delamanid | ||||
pretomanid | ||||
linezolid | ||||
streptomycin | ||||
amikacin | ||||
kanamycin | ||||
capreomycin | ||||
clofazimine | ||||
ethionamide | ||||
para-aminosalicylic_acid | ||||
cycloserine |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761161 | p.Leu452Pro | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | |
pncA | 2289039 | p.Trp68* | stop_gained | 1.0 | pyrazinamide | Assoc w R - interim | |
ahpC | 2726409 | p.Asp73His | missense_variant | 1.0 | isoniazid | Uncertain significance |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
mshA | 576108 | p.Ala254Gly | missense_variant | 0.31 | ethionamide | Uncertain significance |
isoniazid | ||||||
mshA | 576482 | p.Val379Leu | missense_variant | 0.21 | ethionamide | |
isoniazid | ||||||
rpoC | 764584 | c.1215G>A | synonymous_variant | 1.0 | rifampicin | |
rpoC | 765150 | p.Gly594Glu | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 765454 | c.2085C>A | synonymous_variant | 1.0 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.98 | streptomycin | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
katG | 2154678 | c.1434G>C | synonymous_variant | 1.0 | isoniazid | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
fbiD | 3339734 | p.Ala206Gly | missense_variant | 0.4 | delamanid | |
Rv3083 | 3449670 | c.1167C>A | synonymous_variant | 1.0 | ethionamide | |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
alr | 3840911 | c.510A>G | synonymous_variant | 1.0 | cycloserine | |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4246567 | c.54_55insT | frameshift_variant | 0.18 | ethambutol | |
embB | 4246584 | p.Arg24Pro | missense_variant | 0.23 | ethambutol | |
embB | 4249408 | c.2895G>A | synonymous_variant | 1.0 | ethambutol | |
embB | 4249678 | c.3165C>A | synonymous_variant | 1.0 | ethambutol | |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
gid | 4407785 | p.Ala140Pro | missense_variant | 1.0 | streptomycin |