Run ID: SRR1166181
Sample name:
Date: 2024-10-04T20:46:07.332789
Number of reads: 216313
Percentage reads mapped: 6.34
Median coverage: 3.0
Strain: lineage4.2.1
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2 | Euro-American | None | 0.21 |
lineage4 | Euro-American | None | 1.0 |
lineage4.2.1 | Euro-American (TUR) | None | 0.22 |
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 |
---|---|---|---|---|---|---|
rpoB | 762888 | p.His1028Asn | missense_variant | 0.71 | rifampicin | |
rpoB | 762899 | c.3093G>C | synonymous_variant | 0.78 | rifampicin | Not assoc w R - Interim |
rpoB | 762911 | p.Ile1035Met | missense_variant | 0.75 | rifampicin | |
rpoB | 762917 | c.3111C>G | synonymous_variant | 0.75 | rifampicin | Not assoc w R - Interim |
rpoB | 762920 | c.3114C>T | synonymous_variant | 0.75 | rifampicin | Not assoc w R - Interim |
rpoB | 762929 | c.3123G>T | synonymous_variant | 0.81 | rifampicin | Not assoc w R - Interim |
rpoB | 762930 | p.Pro1042Ser | missense_variant | 0.81 | rifampicin | |
rpoC | 762936 | c.-434_-432delTCGinsAGC | upstream_gene_variant | 0.81 | rifampicin | |
rpoB | 762939 | p.Met1045Leu | missense_variant | 0.81 | rifampicin | |
rpoB | 762942 | p.Ile1046Val | missense_variant | 0.83 | rifampicin | Uncertain significance |
rpoC | 762965 | c.-405T>C | upstream_gene_variant | 0.87 | rifampicin | |
rpoC | 762983 | c.-387C>T | upstream_gene_variant | 0.83 | rifampicin | |
rpoB | 762989 | c.3183G>T | synonymous_variant | 0.76 | rifampicin | Not assoc w R - Interim |
rpoB | 763005 | p.Cys1067Val | missense_variant | 0.69 | rifampicin | |
rpoB | 763014 | p.Met1070Leu | missense_variant | 0.75 | rifampicin | |
rpoB | 763017 | p.Gln1071Glu | missense_variant | 0.75 | rifampicin | |
rpoC | 763025 | c.-345C>T | upstream_gene_variant | 0.75 | rifampicin | |
rpoB | 763028 | c.3222T>C | synonymous_variant | 0.75 | rifampicin | Not assoc w R - Interim |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.75 | rifampicin | Not assoc w R |
rpoB | 763034 | c.3228C>G | synonymous_variant | 0.75 | rifampicin | Not assoc w R - Interim |
rrs | 1472177 | n.332C>T | non_coding_transcript_exon_variant | 0.64 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472214 | n.369C>G | non_coding_transcript_exon_variant | 0.62 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472225 | n.380C>A | non_coding_transcript_exon_variant | 0.64 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472235 | n.390G>C | non_coding_transcript_exon_variant | 0.7 | kanamycin | |
capreomycin | ||||||
streptomycin | Uncertain significance | |||||
amikacin | ||||||
rrs | 1472714 | n.869A>C | non_coding_transcript_exon_variant | 0.88 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472715 | n.870C>G | non_coding_transcript_exon_variant | 0.88 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472716 | n.871C>A | non_coding_transcript_exon_variant | 0.89 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472742 | n.897C>T | non_coding_transcript_exon_variant | 0.96 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472754 | n.909G>T | non_coding_transcript_exon_variant | 0.96 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472781 | n.936C>T | non_coding_transcript_exon_variant | 0.97 | 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 | 0.96 | 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 | 0.95 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472824 | n.979T>A | non_coding_transcript_exon_variant | 0.87 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472827 | n.982G>C | non_coding_transcript_exon_variant | 0.84 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472828 | n.983T>C | non_coding_transcript_exon_variant | 0.84 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472839 | n.994C>G | non_coding_transcript_exon_variant | 0.67 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473044 | n.1199C>G | non_coding_transcript_exon_variant | 0.97 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473051 | n.1206T>C | non_coding_transcript_exon_variant | 0.97 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473053 | n.1208T>G | non_coding_transcript_exon_variant | 0.97 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473056 | n.1211A>T | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473062 | n.1217T>A | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473068 | n.1223A>G | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473080 | n.1235C>T | non_coding_transcript_exon_variant | 0.94 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473093 | n.1248C>T | non_coding_transcript_exon_variant | 0.92 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473097 | n.1252G>C | non_coding_transcript_exon_variant | 0.91 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1473099 | n.1254T>A | non_coding_transcript_exon_variant | 0.91 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473147 | n.1302G>C | non_coding_transcript_exon_variant | 0.83 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473148 | n.1303G>A | non_coding_transcript_exon_variant | 0.85 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473163 | n.1318C>T | non_coding_transcript_exon_variant | 0.86 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473164 | n.1319C>G | non_coding_transcript_exon_variant | 0.86 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473177 | n.1332G>A | non_coding_transcript_exon_variant | 0.86 | 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 | 0.78 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473192 | n.1347A>G | non_coding_transcript_exon_variant | 0.78 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1473193 | n.1348G>A | non_coding_transcript_exon_variant | 0.78 | kanamycin | Uncertain significance |
capreomycin | ||||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
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 | 1473204 | n.1359C>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 | 0.78 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473206 | n.1361G>A | non_coding_transcript_exon_variant | 0.78 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475517 | n.1860C>T | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1475518 | n.1861A>G | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475526 | n.1869C>A | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475538 | n.1881T>C | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1475539 | n.1882A>T | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475540 | n.1883C>T | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1475545 | n.1888T>G | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1475550 | n.1893A>C | non_coding_transcript_exon_variant | 0.97 | capreomycin | Uncertain significance |
linezolid | ||||||
rrl | 1475551 | n.1894T>G | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1475555 | n.1898T>G | non_coding_transcript_exon_variant | 0.97 | capreomycin | |
linezolid | ||||||
rrl | 1475564 | n.1907C>A | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
linezolid | ||||||
rrl | 1475574 | n.1917C>G | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
linezolid | ||||||
rrl | 1475576 | n.1919C>A | non_coding_transcript_exon_variant | 0.94 | capreomycin | |
linezolid | ||||||
rrl | 1476336 | n.2679C>T | non_coding_transcript_exon_variant | 0.93 | capreomycin | |
linezolid | ||||||
rrl | 1476356 | n.2699C>A | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | ||||||
rrl | 1476357 | n.2700T>C | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | ||||||
rrl | 1476358 | n.2701T>C | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476359 | n.2702C>G | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476369 | n.2712C>T | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476381 | n.2724G>C | non_coding_transcript_exon_variant | 0.99 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476382 | n.2725A>G | non_coding_transcript_exon_variant | 0.99 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476383 | n.2726T>G | non_coding_transcript_exon_variant | 0.99 | capreomycin | |
linezolid | ||||||
rrl | 1476384 | n.2727G>T | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | ||||||
rrl | 1476408 | n.2751G>A | non_coding_transcript_exon_variant | 0.99 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476411 | n.2754G>A | non_coding_transcript_exon_variant | 0.99 | capreomycin | |
linezolid | ||||||
rrl | 1476425 | n.2768G>A | non_coding_transcript_exon_variant | 0.99 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476429 | n.2772A>C | non_coding_transcript_exon_variant | 0.98 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476442 | n.2785T>A | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | ||||||
rrl | 1476443 | n.2786G>T | non_coding_transcript_exon_variant | 0.98 | capreomycin | |
linezolid | ||||||
rrl | 1476455 | n.2798C>A | non_coding_transcript_exon_variant | 0.99 | capreomycin | |
linezolid | ||||||
rrl | 1476456 | n.2799A>T | non_coding_transcript_exon_variant | 0.99 | capreomycin | |
linezolid | ||||||
rrl | 1476463 | n.2806C>T | non_coding_transcript_exon_variant | 0.99 | capreomycin | |
linezolid | ||||||
rrl | 1476466 | n.2809C>T | non_coding_transcript_exon_variant | 0.99 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476506 | n.2849T>C | non_coding_transcript_exon_variant | 0.92 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476512 | n.2855C>T | non_coding_transcript_exon_variant | 0.88 | capreomycin | Uncertain significance |
linezolid |