Run ID: c96c6954-a459-4929-a0b4-282ea8b02b59
Sample name:
Date: 29-11-2023 05:16:01
Number of reads: 1267891
Percentage reads mapped: 95.61
Median coverage: 28
Strain: La1.4
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
La1 | M.bovis | None | 1.0 |
La1.4 | M.bovis | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | ||||
pyrazinamide | pncA | p.His57Asp | Assoc w R | |
moxifloxacin | gyrA | p.Ala90Val | Assoc w R | |
p.Asp94Gly | Assoc w R | |||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
p.Asp94Gly | Assoc w R | |||
bedaquiline | ||||
delamanid | ||||
pretomanid | ||||
linezolid | ||||
streptomycin | ||||
amikacin | ||||
kanamycin | ||||
capreomycin | ||||
clofazimine | ||||
ethionamide | ||||
para-aminosalicylic_acid | ||||
cycloserine |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.58 | ofloxacin | Uncertain significance | |
moxifloxacin | Assoc w R | ||||||
levofloxacin | Assoc w R | ||||||
fluoroquinolones | Uncertain significance | ||||||
ciprofloxacin | Uncertain significance | ||||||
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.17 | ofloxacin | Uncertain significance | |
moxifloxacin | Assoc w R | ||||||
levofloxacin | Assoc w R | ||||||
fluoroquinolones | Uncertain significance | ||||||
ciprofloxacin | Uncertain significance | ||||||
pncA | 2289073 | p.His57Asp | missense_variant | 1.0 | pyrazinamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5752 | c.513G>A | synonymous_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 6406 | c.-896C>T | 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 | 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 | 7784 | c.483A>G | synonymous_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
ciprofloxacin | ||||||
ofloxacin | ||||||
gyrA | 8243 | c.942C>T | synonymous_variant | 1.0 | fluoroquinolones | |
moxifloxacin | ||||||
levofloxacin | ||||||
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 | 760358 | c.552C>T | synonymous_variant | 0.11 | rifampicin | |
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 | |||||
mmpL5 | 776249 | p.Glu744Asp | missense_variant | 1.0 | clofazimine | |
bedaquiline | ||||||
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 |
fbiC | 1303009 | p.Arg27Trp | missense_variant | 1.0 | delamanid | |
fbiC | 1303242 | c.312T>C | synonymous_variant | 1.0 | delamanid | |
fbiC | 1303545 | c.615A>G | synonymous_variant | 1.0 | delamanid | |
embR | 1416989 | c.358delA | frameshift_variant | 1.0 | ethambutol | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | linezolid | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
aminoglycosides | ||||||
streptomycin | ||||||
rrl | 1473389 | n.-269C>T | upstream_gene_variant | 0.11 | linezolid | |
rrl | 1473996 | n.339C>A | non_coding_transcript_exon_variant | 0.18 | linezolid | |
rrl | 1474315 | n.658A>C | non_coding_transcript_exon_variant | 0.11 | linezolid | |
rpsA | 1834859 | p.Ala440Thr | missense_variant | 1.0 | pyrazinamide | |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | |
ndh | 2103173 | c.-132delG | upstream_gene_variant | 1.0 | ethionamide | |
isoniazid | ||||||
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 | 2168011 | p.Ser868Arg | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
PPE35 | 2168814 | c.1798dupA | frameshift_variant | 1.0 | pyrazinamide | |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.96 | 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 | |
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 | |
ald | 3087364 | p.Asn182Thr | missense_variant | 1.0 | cycloserine | |
Rv3083 | 3448783 | p.Val94Ile | missense_variant | 1.0 | ethionamide | Uncertain significance |
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 | 3474651 | c.645G>T | synonymous_variant | 1.0 | capreomycin | |
amikacin | ||||||
fprA | 3475159 | p.Asn385Asp | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
fbiB | 3640863 | c.-672C>G | upstream_gene_variant | 0.13 | delamanid | |
fbiB | 3642581 | p.Ile349Met | missense_variant | 0.11 | delamanid | |
fbiB | 3642603 | p.Ala357Thr | missense_variant | 1.0 | delamanid | |
rpoA | 3878630 | c.-124delC | upstream_gene_variant | 1.0 | rifampicin | |
clpC1 | 4038403 | c.2302T>C | synonymous_variant | 1.0 | pyrazinamide | |
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 | 4246551 | p.Asn13Ser | missense_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4246864 | c.351C>T | synonymous_variant | 1.0 | ethambutol | |
embB | 4246991 | p.Asn160Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4248469 | c.1956C>T | synonymous_variant | 1.0 | ethambutol | |
aftB | 4267858 | p.Ile327Val | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
aftB | 4269351 | c.-515C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Uncertain significance |
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 |