Run ID: ERR9992734
Sample name:
Date: 2024-10-05T06:11:21.157053
Number of reads: 5207162
Percentage reads mapped: 99.8
Median coverage: 162.0
Strain: lineage4.7
Spoligotype:
Drug-resistance: XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.7 | Euro-American (mainly T) | 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.-154G>A | Assoc w R | Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | p.Gly97Asp | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-154G>A | Assoc w R - Interim | Alias fabG1_p.Leu203Leu |
ethA | p.Thr342Lys | Uncertain significance | Mutation from literature | |
clofazimine | mmpR5 | c.275dupA | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | mmpR5 | c.275dupA | 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 | 7570 | p.Ala90Val | missense_variant | 1.0 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
mmpR5 | 779263 | c.275dupA | frameshift_variant&stop_gained | 1.0 | bedaquiline | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 |
clofazimine | Assoc w R | Can only confer resistance if genetically linked to a functional MmpL5 | |||||
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 1.0 | ethionamide | Assoc w R - Interim | Alias fabG1_p.Leu203Leu |
isoniazid | Assoc w R | Alias fabG1_p.Leu203Leu. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155167 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288952 | p.Gly97Asp | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4326449 | p.Thr342Lys | missense_variant | 1.0 | ethionamide | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13887 | c.-329T>C | upstream_gene_variant | 1.0 | isoniazid | |
Rv0565c | 657497 | c.-27G>A | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 | rifampicin | Uncertain significance |
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 |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474294 | n.637C>G | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249732 | c.3219C>G | synonymous_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 | |||||
gid | 4407704 | p.Ala167Pro | missense_variant | 1.0 | streptomycin | Uncertain significance |