Run ID: SRR1172830
Sample name:
Date: 2024-04-14T14:58:14.944045
Number of reads: 372322
Percentage reads mapped: 95.78
Median coverage: 7.0
Strain: lineage2.2.2
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 1.0 |
lineage2.2.2 | East-Asian (Beijing) | RD105;RD207 | 0.98 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethambutol | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | c.517dupG | Assoc w R | |
streptomycin | rrs | n.514A>C | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
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 | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T |
ethA | p.Ala381Pro | Uncertain significance | Mutation from literature | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | amikacin | Assoc w R | |
kanamycin | Assoc w R | ||||||
capreomycin | Assoc w R | ||||||
inhA | 1673423 | c.-779G>T | upstream_gene_variant | 1.0 | ethionamide | Assoc w R - Interim | Alias fabG1_c.-17G>T |
isoniazid | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
pncA | 2288724 | c.517dupG | frameshift_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247431 | p.Met306Ile | missense_variant | 1.0 | ethambutol | Assoc w R | |
ethA | 4326333 | p.Ala381Pro | 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 | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
whiB6 | 4338794 | c.-273A>G | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin |