Run ID: SRR28339292
Sample name:
Date: 2024-10-03T23:19:12.463684
Number of reads: 3133282
Percentage reads mapped: 99.52
Median coverage: 100.0
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.His445Asp | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethambutol | embB | p.Met306Leu | Assoc w R | |
pyrazinamide | pncA | p.Gln10Arg | Assoc w R | |
streptomycin | rpsL | p.Lys88Gln | Assoc w R - Interim | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Ala | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Ala | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1402C>T | Assoc w R - Interim | |
capreomycin | rrs | n.1402C>T | Assoc w R | |
kanamycin | rrs | n.1402C>T | Assoc w R - Interim | |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Ala | 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 | 761139 | p.His445Asp | missense_variant | 0.97 | rifampicin | Assoc w R | |
rpsL | 781821 | p.Lys88Gln | missense_variant | 1.0 | streptomycin | Assoc w R - Interim | |
rrs | 1473247 | n.1402C>T | non_coding_transcript_exon_variant | 1.0 | amikacin | Assoc w R - Interim | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R - Interim | ||||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
pncA | 2289213 | p.Gln10Arg | missense_variant | 0.99 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Leu | missense_variant | 1.0 | ethambutol | Assoc w R |
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 | |||||
Rv0565c | 656094 | p.Trp459* | stop_gained | 1.0 | ethionamide | Uncertain significance |
rpoB | 760223 | c.417T>C | synonymous_variant | 1.0 | rifampicin | |
rpoC | 764126 | p.Thr253Ser | missense_variant | 1.0 | rifampicin | |
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 |
Rv1129c | 1254517 | c.18C>A | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
katG | 2154629 | p.Gly495Ser | 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 | 1.0 | bedaquiline | |
clofazimine | ||||||
folC | 2747325 | p.Arg92Ser | missense_variant | 1.0 | para-aminosalicylic_acid | |
thyX | 3067949 | c.-4C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
thyA | 3074328 | c.143delA | frameshift_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3087538 | p.Leu240Pro | missense_variant | 1.0 | cycloserine | |
alr | 3841228 | p.Val65Leu | missense_variant | 1.0 | cycloserine | |
glpK | 4138564 | c.1192C>T | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
ubiA | 4269721 | p.Ala38Val | missense_variant | 1.0 | ethambutol | Uncertain significance |
ethA | 4327448 | p.Ile9Thr | missense_variant | 1.0 | ethionamide | Uncertain significance |
whiB6 | 4338397 | p.Thr42Arg | missense_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R |