Run ID: 6835cf1b-13cf-4d30-9e4c-c82b82d41419
Sample name:
Date: 02-08-2023 20:09:32
Number of reads: 642709
Percentage reads mapped: 99.67
Median coverage: 27
Strain: La2
Spoligotype:
Drug-resistance: Sensitive
Lineage | Family | RDs | Frequency |
---|---|---|---|
La2 | M.caprae | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | ||||
moxifloxacin | ||||
levofloxacin | ||||
bedaquiline | ||||
delamanid | ||||
pretomanid | ||||
linezolid | ||||
streptomycin | ||||
amikacin | ||||
kanamycin | ||||
capreomycin | ||||
clofazimine | ||||
ethionamide | ||||
para-aminosalicylic_acid | ||||
cycloserine |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5752 | c.513G>A | synonymous_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrB | 6284 | p.Asp349Asn | missense_variant | 0.11 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 6307 | c.-995T>G | upstream_gene_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrB | 6446 | p.Ala403Ser | missense_variant | 1.0 | fluoroquinolones | |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 6721 | c.-581C>T | upstream_gene_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
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 | 8285 | c.984C>T | synonymous_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
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 | |
rpoB | 762699 | p.Ile965Val | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 763031 | c.-339T>C | upstream_gene_variant | 1.0 | rifampicin | |
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 | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 1.0 | delamanid | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
rrl | 1475406 | n.1749T>C | non_coding_transcript_exon_variant | 0.18 | linezolid | |
rrl | 1475448 | n.1791T>C | non_coding_transcript_exon_variant | 0.14 | linezolid | |
inhA | 1673655 | c.-547C>T | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
inhA | 1673766 | c.-436C>T | upstream_gene_variant | 1.0 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
rpsA | 1834859 | p.Ala440Thr | missense_variant | 1.0 | pyrazinamide | |
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Uncertain significance |
katG | 2155503 | c.609C>T | synonymous_variant | 1.0 | isoniazid | |
katG | 2156025 | c.87C>A | synonymous_variant | 1.0 | isoniazid | |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
PPE35 | 2169479 | p.Asn378Lys | missense_variant | 0.13 | pyrazinamide | |
PPE35 | 2169623 | c.990T>C | synonymous_variant | 0.13 | pyrazinamide | |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
eis | 2714317 | p.Arg339Gln | missense_variant | 1.0 | kanamycin | |
amikacin | ||||||
ald | 3086728 | c.-92C>T | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3087084 | c.266delA | frameshift_variant | 1.0 | cycloserine | |
fprA | 3473996 | c.-11_-10insA | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
fprA | 3474427 | p.Val141Ile | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
whiB7 | 3568838 | c.-159G>A | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | ||||||
amikacin | ||||||
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Uncertain significance |
embA | 4242643 | c.-590C>T | upstream_gene_variant | 1.0 | ethambutol | |
embA | 4242970 | c.-263C>T | upstream_gene_variant | 1.0 | ethambutol | |
embA | 4244220 | c.988C>T | synonymous_variant | 1.0 | ethambutol | |
embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4267858 | p.Ile327Val | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
aftB | 4269132 | c.-296G>A | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
aftB | 4269351 | c.-515C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
aftB | 4269573 | c.-737A>G | upstream_gene_variant | 0.1 | capreomycin | |
amikacin | ||||||
aftB | 4269606 | c.-770T>C | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
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 |