Run ID: SRR4034769
Sample name:
Date: 2024-04-15T08:08:17.100642
Number of reads: 964124
Percentage reads mapped: 27.65
Median coverage: 13.0
Strain: lineage4.1.1.1
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 0.98 |
lineage4.1.1.1 | Euro-American (X-type) | RD183 | 0.32 |
lineage4 | Euro-American | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | None | 0.92 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
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 | 0.91 | streptomycin | 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 | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491342 | p.Arg187His | missense_variant | 0.8 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1472557 | n.712G>A | non_coding_transcript_exon_variant | 0.74 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.72 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472579 | n.734G>T | non_coding_transcript_exon_variant | 0.71 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472581 | n.736A>T | non_coding_transcript_exon_variant | 0.71 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472598 | n.753A>C | non_coding_transcript_exon_variant | 0.72 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472599 | n.754G>T | non_coding_transcript_exon_variant | 0.72 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.73 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472713 | n.868T>C | non_coding_transcript_exon_variant | 0.69 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472716 | n.871C>T | non_coding_transcript_exon_variant | 0.8 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.91 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472744 | n.899A>G | non_coding_transcript_exon_variant | 0.9 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.86 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472793 | n.948A>T | non_coding_transcript_exon_variant | 0.84 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472803 | n.958T>A | non_coding_transcript_exon_variant | 0.81 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473161 | n.1316A>C | non_coding_transcript_exon_variant | 0.22 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.23 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473164 | n.1319C>G | non_coding_transcript_exon_variant | 0.23 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.24 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473172 | n.1327T>C | non_coding_transcript_exon_variant | 0.33 | streptomycin | Not assoc w R |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.36 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.41 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473199 | n.1356delA | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.47 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473352 | n.1507C>T | non_coding_transcript_exon_variant | 0.45 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrl | 1475783 | n.2126T>G | non_coding_transcript_exon_variant | 0.53 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475803 | n.2146T>C | non_coding_transcript_exon_variant | 0.57 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475804 | n.2147G>C | non_coding_transcript_exon_variant | 0.58 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.65 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.63 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475858 | n.2201T>C | non_coding_transcript_exon_variant | 0.52 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475866 | n.2209T>A | non_coding_transcript_exon_variant | 0.55 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476260 | n.2603A>G | non_coding_transcript_exon_variant | 0.35 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476332 | n.2675G>C | non_coding_transcript_exon_variant | 0.86 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476338 | n.2681C>T | non_coding_transcript_exon_variant | 0.89 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476353 | n.2696G>T | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.93 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476372 | n.2715T>C | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.96 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>A | non_coding_transcript_exon_variant | 0.95 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476425 | n.2768G>T | non_coding_transcript_exon_variant | 0.94 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.93 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.93 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476481 | n.2824T>C | non_coding_transcript_exon_variant | 0.87 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.82 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476514 | n.2857C>T | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476519 | n.2862C>G | non_coding_transcript_exon_variant | 0.78 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476524 | n.2867C>T | non_coding_transcript_exon_variant | 0.77 | capreomycin | |
linezolid | ||||||
rrl | 1476525 | n.2868A>G | non_coding_transcript_exon_variant | 0.81 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476530 | n.2873C>T | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476536 | n.2879G>A | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476537 | n.2880A>G | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476538 | n.2881A>G | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476540 | n.2883C>G | non_coding_transcript_exon_variant | 0.74 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476547 | n.2890C>T | non_coding_transcript_exon_variant | 0.78 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476567 | n.2910C>T | non_coding_transcript_exon_variant | 0.85 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476572 | n.2915G>T | non_coding_transcript_exon_variant | 0.74 | capreomycin | |
linezolid | ||||||
rrl | 1476573 | n.2916A>T | non_coding_transcript_exon_variant | 0.69 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1476577 | n.2920T>G | non_coding_transcript_exon_variant | 0.69 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476584 | n.2927C>T | non_coding_transcript_exon_variant | 0.69 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | 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 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin |