Run ID: SRR13591376
Sample name:
Date: 2024-10-04T04:07:38.775214
Number of reads: 3157224
Percentage reads mapped: 29.67
Median coverage: 67.5
Strain: lineage4.3.2
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 1.0 |
lineage4.3.2 | Euro-American (LAM) | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
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 |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.98 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mshA | 575350 | p.Met1? | start_lost | 1.0 | isoniazid | Uncertain significance |
ethionamide | Uncertain significance | |||||
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
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 | 1254556 | c.-22A>G | upstream_gene_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.31 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.4 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.42 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472153 | n.308G>A | non_coding_transcript_exon_variant | 0.43 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.49 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.52 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.63 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.56 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.55 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.47 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472252 | n.407G>A | non_coding_transcript_exon_variant | 0.47 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.47 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472256 | n.411T>A | non_coding_transcript_exon_variant | 0.47 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.48 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 0.96 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R | |||||
rrs | 1472541 | n.696T>G | non_coding_transcript_exon_variant | 0.28 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.42 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472553 | n.708C>T | non_coding_transcript_exon_variant | 0.52 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.53 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472572 | n.727T>C | non_coding_transcript_exon_variant | 0.52 | kanamycin | Uncertain significance |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472574 | n.729T>C | non_coding_transcript_exon_variant | 0.52 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472579 | n.734G>A | non_coding_transcript_exon_variant | 0.53 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472582 | n.737G>A | non_coding_transcript_exon_variant | 0.53 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472583 | n.738T>A | non_coding_transcript_exon_variant | 0.52 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472584 | n.739A>G | non_coding_transcript_exon_variant | 0.52 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472594 | n.749G>C | non_coding_transcript_exon_variant | 0.54 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472598 | n.753A>T | non_coding_transcript_exon_variant | 0.54 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.55 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.28 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.7 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.68 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.69 | 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 | 0.64 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473139 | n.1294T>C | non_coding_transcript_exon_variant | 0.31 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.37 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.42 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.51 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.5 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.53 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473191 | n.1346C>T | non_coding_transcript_exon_variant | 0.55 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.55 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.54 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.55 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.54 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473206 | n.1361G>A | non_coding_transcript_exon_variant | 0.54 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475538 | n.1881T>C | non_coding_transcript_exon_variant | 0.31 | capreomycin | |
linezolid | ||||||
rrl | 1475539 | n.1882A>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475540 | n.1883C>T | non_coding_transcript_exon_variant | 0.31 | capreomycin | |
linezolid | ||||||
rrl | 1475545 | n.1888T>G | non_coding_transcript_exon_variant | 0.3 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475550 | n.1893A>C | non_coding_transcript_exon_variant | 0.29 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475551 | n.1894T>G | non_coding_transcript_exon_variant | 0.3 | capreomycin | |
linezolid | ||||||
rrl | 1475555 | n.1898T>G | non_coding_transcript_exon_variant | 0.3 | capreomycin | |
linezolid | ||||||
rrl | 1475564 | n.1907C>A | non_coding_transcript_exon_variant | 0.31 | capreomycin | |
linezolid | ||||||
rrl | 1475574 | n.1917C>G | non_coding_transcript_exon_variant | 0.32 | capreomycin | |
linezolid | ||||||
rrl | 1475575 | n.1918C>T | non_coding_transcript_exon_variant | 0.32 | capreomycin | |
linezolid | ||||||
rrl | 1475576 | n.1919C>G | non_coding_transcript_exon_variant | 0.32 | capreomycin | |
linezolid | ||||||
rrl | 1475816 | n.2159C>G | non_coding_transcript_exon_variant | 0.13 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475817 | n.2160A>G | non_coding_transcript_exon_variant | 0.14 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.71 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.75 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.75 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.75 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.75 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.76 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.77 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.77 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.77 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.77 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.82 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.82 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.79 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.8 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.77 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.76 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.75 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.74 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.74 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.75 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.53 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.37 | capreomycin | Uncertain significance |
linezolid | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2477c | 2782827 | p.Val406Phe | missense_variant | 1.0 | kanamycin | Uncertain significance |
levofloxacin | Uncertain significance | |||||
moxifloxacin | Uncertain significance | |||||
streptomycin | ||||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
lpqB | 3623794 | p.Ala373Ser | missense_variant | 1.0 | rifampicin | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
clpC1 | 4040072 | c.633C>T | synonymous_variant | 1.0 | pyrazinamide | |
embC | 4242643 | c.2781C>T | 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 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |