Run ID: DRR130198
Sample name:
Date: 2025-03-07T09:37:14.884295
Number of reads: 1590368
Percentage reads mapped: 99.8
Median coverage: 83.0
Strain: lineage4.9
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.9 | Euro-American (H37Rv-like) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.His445Arg | Assoc w R | |
isoniazid | ||||
ethambutol | ||||
pyrazinamide | pncA | c.164_167dupGTGA | 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 | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
kanamycin | rrs | n.1401A>G | Assoc w R | |
cycloserine | ||||
ethionamide | ethA | c.611_627dupTGCTGCAGCGCTCACCC | Assoc w R | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.99 | 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 | 761140 | p.His445Arg | missense_variant | 0.98 | rifampicin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
pncA | 2289074 | c.164_167dupGTGA | frameshift_variant&stop_gained | 1.0 | pyrazinamide | Assoc w R | |
ethA | 4326846 | c.611_627dupTGCTGCAGCGCTCACCC | frameshift_variant | 1.0 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1242 | c.1242G>A | synonymous_variant | 0.99 | isoniazid | Uncertain significance |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mshA | 576220 | c.877dupG | frameshift_variant | 1.0 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
rpoC | 764894 | p.Ile509Val | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 766203 | p.Gly945Asp | 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 | amikacin | Uncertain significance |
capreomycin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
katG | 2154393 | p.Asp573Ala | missense_variant | 1.0 | isoniazid | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223724 | c.-560C>G | upstream_gene_variant | 0.98 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
ahpC | 2726105 | c.-88_-87insAT | upstream_gene_variant | 0.99 | isoniazid | Uncertain significance |
Rv3236c | 3612486 | p.Thr211Pro | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | amikacin | Not assoc w R |
capreomycin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
gid | 4408070 | p.Trp45Gly | missense_variant | 1.0 | streptomycin | Uncertain significance |