Run ID: ERR9993083
Sample name:
Date: 2024-03-25T21:13:52.130119
Number of reads: 5380618
Percentage reads mapped: 99.6
Median coverage: 166.0
Strain: lineage4.1.1.3
Spoligotype:
Drug-resistance: XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | RD193 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
rpoC | p.Phe452Ser | Uncertain significance | Mutation from literature | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ahpC | c.-48G>A | Uncertain significance | Mutation from literature | |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | p.Val139Met | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Asn | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Asn | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.597delC | Assoc w R | |
clofazimine | mmpR5 | c.144dupC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
c.177dupG | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | ||
c.319dupC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | ||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | mmpR5 | c.144dupC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
c.177dupG | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | ||
c.319dupC | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | ||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Asn | missense_variant | 0.92 | moxifloxacin | Assoc w R | High-level resistance |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpoC | 764724 | p.Phe452Ser | missense_variant | 1.0 | rifampicin | Uncertain significance | Mutation from literature |
mmpR5 | 779130 | c.144dupC | frameshift_variant | 0.28 | clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | |||||
mmpR5 | 779165 | c.177dupG | frameshift_variant | 0.4 | clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | |||||
mmpR5 | 779307 | c.319dupC | frameshift_variant | 0.21 | clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | |||||
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2155167 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288827 | p.Val139Met | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4326876 | c.597delC | frameshift_variant | 1.0 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6608 | p.Val457Leu | 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 | |||||
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 | 0.99 | 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 | 800219 | c.-590T>C | upstream_gene_variant | 1.0 | linezolid | |
rplC | 801354 | c.546G>A | synonymous_variant | 1.0 | linezolid | Not assoc w R - Interim |
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 |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3449616 | p.Met371Ile | missense_variant | 1.0 | ethionamide | Uncertain significance |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
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 |
embB | 4249408 | c.2895G>A | 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 |