Run ID: 9b9a54ce-96e9-400e-8272-095e2af9d718
Sample name:
Date: 27-02-2023 12:56:38
Number of reads: 1504295
Percentage reads mapped: 98.91
Median coverage: 49
Strain: lineage2.2.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 1.0 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 1.0 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | p.Ile133Thr | Assoc w R | |
moxifloxacin | gyrA | p.Ser91Pro | Assoc w R | |
levofloxacin | gyrA | p.Ser91Pro | Assoc w R | |
bedaquiline | ||||
delamanid | ||||
pretomanid | ||||
linezolid | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
amikacin | rrs | n.1401A>G | Assoc w R | |
kanamycin | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
clofazimine | ||||
ethionamide | ||||
para-aminosalicylic_acid | ||||
cycloserine |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7572 | p.Ser91Pro | missense_variant | 1.0 | ofloxacin | Uncertain significance | |
moxifloxacin | Assoc w R | ||||||
levofloxacin | Assoc w R | ||||||
fluoroquinolones | Uncertain significance | ||||||
ciprofloxacin | Uncertain significance | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 1.0 | kanamycin | Assoc w R | |
capreomycin | Assoc w R | ||||||
aminoglycosides | Uncertain significance | ||||||
amikacin | Assoc w R | ||||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | |
pncA | 2288844 | p.Ile133Thr | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 1.0 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | delamanid | |
mshA | 575907 | p.Ala187Val | missense_variant | 1.0 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.98 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 | rifampicin | |
rpoC | 764817 | p.Val483Gly | missense_variant | 1.0 | rifampicin | |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 1.0 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 1.0 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
rrl | 1473927 | n.270C>T | non_coding_transcript_exon_variant | 0.18 | linezolid | |
rrl | 1474639 | n.982G>A | non_coding_transcript_exon_variant | 0.17 | linezolid | Uncertain significance |
rrl | 1474948 | n.1291C>T | non_coding_transcript_exon_variant | 0.13 | linezolid | |
rpsA | 1834177 | c.636A>C | synonymous_variant | 1.0 | pyrazinamide | |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
embA | 4243460 | c.228C>T | synonymous_variant | 1.0 | ethambutol | |
aftB | 4267635 | p.Arg401Gln | missense_variant | 0.11 | capreomycin | |
amikacin | ||||||
aftB | 4267647 | p.Asp397Gly | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
aftB | 4267889 | c.948C>T | synonymous_variant | 0.13 | capreomycin | |
amikacin | ||||||
aftB | 4268862 | c.-26G>A | upstream_gene_variant | 0.12 | capreomycin | |
amikacin | ||||||
ethA | 4326450 | p.Thr342Ala | missense_variant | 1.0 | ethionamide | Uncertain significance |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.98 | streptomycin | Uncertain significance |