Run ID: ERR036211
Sample name:
Date: 2024-04-15T15:49:40.729765
Number of reads: 1168771
Percentage reads mapped: 93.55
Median coverage: 20.0
Strain: lineage1.1.3.2;lineage4.3.4.2.1;lineage4.9
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.4 |
lineage1.1.3 | Indo-Oceanic | RD239 | 0.14 |
lineage1.1.3.2 | Indo-Oceanic | RD239 | 0.07 |
lineage1.1 | Indo-Oceanic | RD239 | 0.06 |
lineage4 | Euro-American | None | 0.69 |
lineage4.3.4.2.1 | Euro-American (LAM) | RD174 | 0.51 |
lineage1 | Indo-Oceanic | RD239 | 0.19 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.09 |
lineage4.3.4 | Euro-American (LAM) | RD174 | 0.56 |
lineage4.3.4.2 | Euro-American (LAM) | RD174 | 0.42 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
streptomycin | ||||
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 |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6140 | p.Val301Leu | missense_variant | 0.3 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.92 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.95 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.41 | isoniazid | Not assoc w R |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.35 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.59 | rifampicin | Not assoc w R |
rpoC | 765230 | p.Ala621Thr | missense_variant | 0.32 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.29 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.19 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.24 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.28 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.45 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.35 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.35 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
tsnR | 1854045 | p.Tyr147Cys | missense_variant | 0.39 | linezolid | Not assoc w R |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.87 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
bacA | 2062922 | p.Ile603Val | missense_variant | 0.32 | streptomycin | Not assoc w R |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.42 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.38 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.32 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.47 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.92 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.88 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.5 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 0.9 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.35 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 0.84 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4408156 | p.Leu16Arg | missense_variant | 0.55 | streptomycin | Not assoc w R |