Run ID: ERR4821880
Sample name:
Date: 2024-10-05T00:35:24.204898
Number of reads: 392756
Percentage reads mapped: 82.02
Median coverage: 7.0
Strain: lineage1.1.2
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.1.2 | Indo-Oceanic | RD239 | 0.95 |
lineage1.1 | Indo-Oceanic | RD239 | 0.99 |
lineage1 | Indo-Oceanic | RD239 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.888G>A | Uncertain significance | Mutation from literature |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rrs | 1472733 | n.888G>A | non_coding_transcript_exon_variant | 0.92 | streptomycin | Uncertain significance | Mutation from literature |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 8452 | p.Ala384Val | missense_variant | 0.73 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.92 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.94 | isoniazid | Not assoc w R |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.9 | ethambutol | |
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.92 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.92 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.93 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.86 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.67 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.93 | isoniazid | |
ahpC | 2726468 | c.276G>A | synonymous_variant | 0.9 | isoniazid | Not assoc w R - Interim |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612581 | p.Leu179Pro | missense_variant | 1.0 | pyrazinamide | |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.75 | ethambutol | Not assoc w R |
embA | 4243848 | p.Val206Met | missense_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | 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 | |||||
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.8 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |