Run ID: ERR4012004
Sample name:
Date: 2024-10-05T09:52:18.925109
Number of reads: 1685279
Percentage reads mapped: 99.6
Median coverage: 52.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 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) |
p.Ser94Ala | Assoc w R - Interim | 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.Pro404Ser | Uncertain significance | Mutation from literature |
pyrazinamide | pncA | c.468_499delGGTGGACCTGACAGCGGGTGTGTCGGCCGATA | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Ile486Leu | Uncertain significance | Mutation from literature |
ofloxacin | ||||
levofloxacin | gyrB | p.Ile486Leu | Uncertain significance | Mutation from literature |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-154G>A | Assoc w R - Interim | Alias fabG1_p.Leu203Leu |
p.Ser94Ala | Assoc w R - Interim | |||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6695 | p.Ile486Leu | missense_variant | 1.0 | levofloxacin | Uncertain significance | Mutation from literature |
moxifloxacin | Uncertain significance | Mutation from literature | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
inhA | 1674048 | c.-154G>A | upstream_gene_variant | 0.95 | 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) | |||||
inhA | 1674481 | p.Ser94Ala | missense_variant | 1.0 | ethionamide | Assoc w R - Interim | |
isoniazid | Assoc w R - Interim | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288742 | c.468_499delGGTGGACCTGACAGCGGGTGTGTCGGCCGATA | frameshift_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247723 | p.Pro404Ser | missense_variant | 1.0 | ethambutol | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 371 | p.Pro124Leu | missense_variant | 0.95 | isoniazid | Not assoc w R |
gyrB | 6743 | p.Val502Phe | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | ||||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
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 |
fbiC | 1305471 | c.2541C>T | synonymous_variant | 1.0 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 1.0 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
PPE35 | 2168867 | c.1746G>A | synonymous_variant | 1.0 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
pncA | 2288742 | c.467_499delNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNC | disruptive_inframe_deletion | 1.0 | pyrazinamide | |
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 0.99 | ethionamide | Uncertain significance |
lpqB | 3624722 | c.189C>T | synonymous_variant | 0.98 | rifampicin | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
alr | 3840764 | c.657G>C | synonymous_variant | 0.98 | cycloserine | |
embC | 4242643 | c.2781C>T | 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 |