Run ID: SRR13591377
Sample name:
Date: 2024-10-04T02:22:35.503580
Number of reads: 584543
Percentage reads mapped: 12.3
Median coverage: 13.0
Strain: lineage4.1.1.3
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.1 | Euro-American | None | 1.0 |
lineage4.1.1.3 | Euro-American (X-type) | RD193 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.1.1 | Euro-American (X-type) | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
rplC | 800219 | c.-590T>C | upstream_gene_variant | 1.0 | linezolid | |
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.55 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472147 | n.302G>A | non_coding_transcript_exon_variant | 0.64 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.68 | 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 | 0.7 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472164 | n.319G>A | non_coding_transcript_exon_variant | 0.73 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.76 | 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 | 0.83 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472240 | n.395G>C | non_coding_transcript_exon_variant | 0.78 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472242 | n.397C>T | non_coding_transcript_exon_variant | 0.78 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472251 | n.406G>T | non_coding_transcript_exon_variant | 0.75 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472252 | n.407G>A | non_coding_transcript_exon_variant | 0.74 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472253 | n.408G>T | non_coding_transcript_exon_variant | 0.74 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472256 | n.411T>A | non_coding_transcript_exon_variant | 0.74 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472259 | n.414C>A | non_coding_transcript_exon_variant | 0.74 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472530 | n.685G>A | non_coding_transcript_exon_variant | 0.32 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472537 | n.692C>T | non_coding_transcript_exon_variant | 0.33 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472541 | n.696T>G | non_coding_transcript_exon_variant | 0.59 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472545 | n.700A>T | non_coding_transcript_exon_variant | 0.69 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472553 | n.708C>T | non_coding_transcript_exon_variant | 0.77 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472571 | n.726G>C | non_coding_transcript_exon_variant | 0.75 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472572 | n.727T>C | non_coding_transcript_exon_variant | 0.74 | kanamycin | Uncertain significance |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472574 | n.729T>C | non_coding_transcript_exon_variant | 0.74 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472579 | n.734G>A | non_coding_transcript_exon_variant | 0.73 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472582 | n.737G>A | non_coding_transcript_exon_variant | 0.73 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472583 | n.738T>A | non_coding_transcript_exon_variant | 0.73 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472584 | n.739A>G | non_coding_transcript_exon_variant | 0.73 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472594 | n.749G>C | non_coding_transcript_exon_variant | 0.77 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472598 | n.753A>T | non_coding_transcript_exon_variant | 0.77 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472616 | n.771G>A | non_coding_transcript_exon_variant | 0.76 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472707 | n.862A>G | non_coding_transcript_exon_variant | 0.59 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472714 | n.869A>C | non_coding_transcript_exon_variant | 0.59 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.61 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.63 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.91 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.91 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.9 | 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 | 0.89 | 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 | 0.58 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473145 | n.1300C>T | non_coding_transcript_exon_variant | 0.63 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.71 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.77 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473166 | n.1321G>A | non_coding_transcript_exon_variant | 0.77 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.79 | 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 | 0.8 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473198 | n.1354delC | non_coding_transcript_exon_variant | 0.78 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473202 | n.1357C>T | non_coding_transcript_exon_variant | 0.78 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrs | 1473205 | n.1360T>C | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473206 | n.1361G>A | non_coding_transcript_exon_variant | 0.8 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475538 | n.1881T>C | non_coding_transcript_exon_variant | 0.64 | capreomycin | |
linezolid | ||||||
rrl | 1475539 | n.1882A>T | non_coding_transcript_exon_variant | 0.64 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475540 | n.1883C>T | non_coding_transcript_exon_variant | 0.62 | capreomycin | |
linezolid | ||||||
rrl | 1475545 | n.1888T>G | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475550 | n.1893A>C | non_coding_transcript_exon_variant | 0.62 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475551 | n.1894T>G | non_coding_transcript_exon_variant | 0.64 | capreomycin | |
linezolid | ||||||
rrl | 1475555 | n.1898T>G | non_coding_transcript_exon_variant | 0.61 | capreomycin | |
linezolid | ||||||
rrl | 1475564 | n.1907C>A | non_coding_transcript_exon_variant | 0.58 | capreomycin | |
linezolid | ||||||
rrl | 1475574 | n.1917C>G | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
linezolid | ||||||
rrl | 1475575 | n.1918C>T | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
linezolid | ||||||
rrl | 1475576 | n.1919C>G | non_coding_transcript_exon_variant | 0.57 | capreomycin | |
linezolid | ||||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.89 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.9 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.89 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.9 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.89 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.91 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.91 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.91 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.91 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.93 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.93 | 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 | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.92 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.92 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.91 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.91 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.91 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.92 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.76 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.53 | capreomycin | Uncertain significance |
linezolid | ||||||
tlyA | 1918081 | p.Asp48Asn | missense_variant | 1.0 | capreomycin | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
pncA | 2289017 | c.225T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
embC | 4242803 | p.Val981Leu | missense_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249408 | c.2895G>A | 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 |