Run ID: ERR4817628
Sample name:
Date: 2024-04-14T23:53:11.669102
Number of reads: 5491408
Percentage reads mapped: 91.2
Median coverage: 98.0
Strain: lineage4.8
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 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 |
---|---|---|---|---|---|---|
dnaA | 371 | p.Pro124Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
dnaA | 1044 | p.Met348Ile | missense_variant | 1.0 | isoniazid | Uncertain significance |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8897 | c.1596T>C | synonymous_variant | 0.1 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 8915 | c.1614A>G | synonymous_variant | 0.1 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
Rv0565c | 656261 | p.Arg404Trp | missense_variant | 1.0 | ethionamide | |
rpoB | 760376 | p.Asp190Glu | missense_variant | 0.11 | rifampicin | Uncertain significance |
rpoB | 760380 | p.Thr192Pro | missense_variant | 0.12 | rifampicin | |
rpoB | 760400 | c.594G>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 760407 | p.Ser201Ala | missense_variant | 0.15 | rifampicin | |
rpoB | 760430 | c.624T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 760436 | c.630C>G | synonymous_variant | 0.16 | rifampicin | |
rpoB | 760460 | c.654G>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoB | 760475 | c.669A>G | synonymous_variant | 0.1 | rifampicin | Not assoc w R - Interim |
rpoB | 760508 | c.702G>C | synonymous_variant | 0.13 | rifampicin | |
rpoB | 760511 | c.705G>C | synonymous_variant | 0.13 | rifampicin | |
rpoB | 760514 | c.708C>G | synonymous_variant | 0.13 | rifampicin | |
rpoB | 760532 | c.726T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 760533 | p.Val243Leu | missense_variant | 0.13 | rifampicin | |
rpoB | 760541 | c.735G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoB | 760547 | c.741G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoB | 760553 | c.747C>G | synonymous_variant | 0.15 | rifampicin | |
rpoB | 760565 | c.759A>C | synonymous_variant | 0.12 | rifampicin | |
rpoB | 760568 | c.762G>C | synonymous_variant | 0.13 | rifampicin | |
rpoB | 760571 | c.765G>C | synonymous_variant | 0.12 | rifampicin | |
rpoB | 761174 | c.1368T>C | synonymous_variant | 0.11 | rifampicin | |
rpoB | 761180 | c.1374A>G | synonymous_variant | 0.11 | rifampicin | |
rpoB | 761189 | c.1383T>C | synonymous_variant | 0.11 | rifampicin | Not assoc w R - Interim |
rpoB | 761192 | c.1386C>G | synonymous_variant | 0.11 | rifampicin | |
rpoB | 761198 | c.1392G>C | synonymous_variant | 0.11 | rifampicin | Not assoc w R - Interim |
rpoB | 761213 | c.1407G>C | synonymous_variant | 0.12 | rifampicin | |
rpoB | 761234 | c.1428G>C | synonymous_variant | 0.1 | rifampicin | Not assoc w R - Interim |
rpoC | 763546 | c.177A>G | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 763558 | c.189C>T | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 763570 | c.201G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 763573 | c.204G>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 763696 | c.327T>C | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 763699 | c.330G>C | synonymous_variant | 0.13 | rifampicin | |
rpoC | 763702 | c.333C>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R - Interim |
rpoC | 763708 | c.339G>C | synonymous_variant | 0.14 | rifampicin | |
rpoC | 763714 | c.345G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 763717 | c.348T>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 763732 | c.363C>G | synonymous_variant | 0.15 | rifampicin | |
rpoC | 763735 | c.366G>C | synonymous_variant | 0.16 | rifampicin | |
rpoC | 763741 | c.372C>T | synonymous_variant | 0.16 | rifampicin | |
rpoC | 763744 | c.375G>C | synonymous_variant | 0.16 | rifampicin | |
rpoC | 764308 | c.939G>C | synonymous_variant | 0.1 | rifampicin | |
rpoC | 764320 | c.951C>G | synonymous_variant | 0.11 | rifampicin | |
rpoC | 764353 | c.984G>C | synonymous_variant | 0.12 | rifampicin | |
rpoC | 764387 | c.1018T>C | synonymous_variant | 0.11 | rifampicin | Not assoc w R - Interim |
rpoC | 764404 | c.1035C>T | synonymous_variant | 0.1 | rifampicin | Not assoc w R - Interim |
rpoC | 764405 | c.1036_1038delAGGinsCC | frameshift_variant&missense_variant | 0.11 | rifampicin | |
rpoC | 764548 | c.1179G>A | synonymous_variant | 0.11 | rifampicin | |
rpoC | 764560 | c.1191T>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 764632 | c.1263T>C | synonymous_variant | 0.12 | rifampicin | Not assoc w R - Interim |
rpoC | 764635 | c.1266C>G | synonymous_variant | 0.12 | rifampicin | |
rpoC | 764695 | c.1326T>C | synonymous_variant | 0.11 | rifampicin | |
rpoC | 764701 | c.1332C>G | synonymous_variant | 0.11 | rifampicin | Not assoc w R - Interim |
rpoC | 764716 | c.1347G>C | synonymous_variant | 0.13 | rifampicin | Not assoc w R - Interim |
rpoC | 764746 | c.1377G>C | synonymous_variant | 0.13 | rifampicin | |
rpoC | 764755 | c.1386C>T | synonymous_variant | 0.13 | rifampicin | |
rpoC | 764764 | c.1395T>C | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
rpoC | 764780 | c.1411_1413delAGCinsTCG | synonymous_variant | 0.15 | rifampicin | |
rpoC | 764797 | c.1428G>C | synonymous_variant | 0.15 | rifampicin | |
rpoC | 764803 | c.1434C>G | synonymous_variant | 0.17 | rifampicin | |
rpoC | 764812 | c.1443C>G | synonymous_variant | 0.16 | rifampicin | |
rpoC | 764815 | c.1446A>G | synonymous_variant | 0.15 | rifampicin | Not assoc w R - Interim |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 | streptomycin | Not assoc w R |
rpsL | 781802 | c.243G>C | synonymous_variant | 0.11 | streptomycin | |
rpsL | 781805 | c.246G>C | synonymous_variant | 0.11 | streptomycin | |
rpsL | 781808 | c.249C>T | synonymous_variant | 0.12 | streptomycin | |
rpsL | 781814 | c.255C>T | synonymous_variant | 0.11 | streptomycin | |
rpsL | 781817 | c.258G>T | synonymous_variant | 0.11 | streptomycin | |
rpsL | 781829 | c.270G>C | synonymous_variant | 0.13 | streptomycin | |
rpsL | 781832 | c.273T>G | synonymous_variant | 0.14 | streptomycin | |
rpsL | 781838 | c.279G>T | synonymous_variant | 0.13 | streptomycin | |
rpsL | 781841 | c.282C>T | synonymous_variant | 0.11 | streptomycin | |
rpsL | 781865 | c.306G>C | synonymous_variant | 0.13 | streptomycin | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1471918 | n.73A>T | non_coding_transcript_exon_variant | 0.17 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1471923 | n.78T>C | non_coding_transcript_exon_variant | 0.18 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1471925 | n.80T>C | non_coding_transcript_exon_variant | 0.18 | streptomycin | |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1471932 | n.87A>G | non_coding_transcript_exon_variant | 0.23 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1471934 | n.89A>G | non_coding_transcript_exon_variant | 0.23 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1471938 | n.93T>A | non_coding_transcript_exon_variant | 0.24 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472106 | n.261G>A | non_coding_transcript_exon_variant | 0.32 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
rrs | 1472108 | n.263C>T | non_coding_transcript_exon_variant | 0.32 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472148 | n.303T>C | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472150 | n.305T>A | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472172 | n.327T>C | non_coding_transcript_exon_variant | 0.48 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
rrs | 1472612 | n.767G>T | non_coding_transcript_exon_variant | 0.77 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473276 | n.1431A>G | non_coding_transcript_exon_variant | 0.38 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1473316 | n.1471C>T | non_coding_transcript_exon_variant | 0.24 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrl | 1475916 | n.2259C>G | non_coding_transcript_exon_variant | 0.64 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476160 | n.2503T>C | non_coding_transcript_exon_variant | 0.32 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rrl | 1476194 | n.2537A>G | non_coding_transcript_exon_variant | 0.37 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476200 | n.2543A>T | non_coding_transcript_exon_variant | 0.39 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476201 | n.2544C>T | non_coding_transcript_exon_variant | 0.41 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476428 | n.2771C>T | non_coding_transcript_exon_variant | 0.48 | capreomycin | Not assoc w R |
linezolid | Uncertain significance | |||||
rrl | 1476524 | n.2867C>T | non_coding_transcript_exon_variant | 0.25 | capreomycin | |
linezolid | ||||||
rrl | 1476529 | n.2872A>T | non_coding_transcript_exon_variant | 0.22 | capreomycin | Uncertain significance |
linezolid | ||||||
rpsA | 1833894 | p.Ala118Glu | missense_variant | 0.11 | pyrazinamide | |
rpsA | 1833952 | c.411C>T | synonymous_variant | 0.11 | pyrazinamide | |
rpsA | 1834340 | p.Met267Leu | missense_variant | 0.1 | pyrazinamide | Uncertain significance |
rpsA | 1834348 | c.807T>C | synonymous_variant | 0.11 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834423 | c.882G>C | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834435 | c.894G>C | synonymous_variant | 0.12 | pyrazinamide | |
rpsA | 1834451 | c.910_912delTTGinsCC | frameshift_variant&missense_variant | 0.14 | pyrazinamide | Uncertain significance |
rpsA | 1834456 | c.915T>C | synonymous_variant | 0.13 | pyrazinamide | |
rpsA | 1834465 | c.924T>C | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834468 | c.927A>G | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834489 | c.948T>C | synonymous_variant | 0.15 | pyrazinamide | |
rpsA | 1834501 | c.960G>C | synonymous_variant | 0.14 | pyrazinamide | |
rpsA | 1834504 | c.963G>C | synonymous_variant | 0.12 | pyrazinamide | |
rpsA | 1834513 | c.972C>G | synonymous_variant | 0.1 | pyrazinamide | |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
katG | 2155098 | c.1014C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
Rv1979c | 2222717 | p.Ala150Pro | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv3083 | 3448507 | c.5_*1408del | frameshift_variant&stop_lost&splice_region_variant | 1.0 | ethionamide | Uncertain significance |
alr | 3840764 | c.657G>C | synonymous_variant | 1.0 | cycloserine | |
clpC1 | 4038808 | c.1896_1897insC | frameshift_variant | 0.14 | pyrazinamide | |
clpC1 | 4038811 | c.1893delT | frameshift_variant | 0.13 | pyrazinamide | |
clpC1 | 4038860 | c.1845G>T | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4038878 | c.1827A>G | synonymous_variant | 0.14 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4038896 | c.1809C>G | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4039004 | c.1701C>G | synonymous_variant | 0.11 | pyrazinamide | |
clpC1 | 4039016 | c.1689C>G | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4039022 | c.1683A>G | synonymous_variant | 0.13 | pyrazinamide | |
clpC1 | 4039085 | c.1620A>G | synonymous_variant | 0.11 | pyrazinamide | |
clpC1 | 4039091 | c.1614G>C | synonymous_variant | 0.11 | pyrazinamide | |
clpC1 | 4039724 | c.981A>G | synonymous_variant | 0.14 | pyrazinamide | |
clpC1 | 4039748 | c.957G>C | synonymous_variant | 0.11 | pyrazinamide | |
clpC1 | 4039751 | c.954A>G | synonymous_variant | 0.12 | pyrazinamide | |
clpC1 | 4039757 | c.948A>G | synonymous_variant | 0.12 | pyrazinamide | |
clpC1 | 4039766 | c.939T>C | synonymous_variant | 0.12 | pyrazinamide | |
clpC1 | 4039769 | c.936C>G | synonymous_variant | 0.12 | pyrazinamide | |
clpC1 | 4039778 | c.927A>G | synonymous_variant | 0.11 | pyrazinamide | |
clpC1 | 4039781 | c.924G>C | synonymous_variant | 0.12 | pyrazinamide | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4246697 | p.Gly62Arg | missense_variant | 1.0 | ethambutol | Uncertain significance |
whiB6 | 4338416 | p.Gln36* | stop_gained | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
gid | 4407535 | p.Thr223Arg | missense_variant | 1.0 | streptomycin |