Run ID: SRR8758879
Sample name:
Date: 2024-03-27T00:10:20.833865
Number of reads: 5462245
Percentage reads mapped: 98.36
Median coverage: 140.0
Strain: lineage1.2.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.2.2.1 | Indo-Oceanic | RD239 | 1.0 |
lineage1.2.2 | Indo-Oceanic | RD239 | 1.0 |
lineage1 | Indo-Oceanic | RD239 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Val | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rrs | n.517C>T | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | folC | p.Ile43Thr | Mutation from literature | |
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761110 | p.Asp435Val | missense_variant | 0.99 | rifampicin | Assoc w R | |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.99 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
folC | 2747471 | p.Ile43Thr | missense_variant | 1.0 | para-aminosalicylic_acid | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 237 | c.237G>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6112 | p.Met291Ile | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.99 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8452 | p.Ala384Val | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8489 | c.1188A>G | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13298 | p.Ile87Met | missense_variant | 0.99 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 1.0 | isoniazid | Not assoc w R |
fgd1 | 491060 | p.Met93Thr | missense_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
ccsA | 620659 | p.Arg257Cys | missense_variant | 1.0 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 1.0 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 1.0 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 763884 | p.Ala172Val | missense_variant | 0.99 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.98 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 0.99 | linezolid | Not assoc w R |
rplC | 800899 | p.Ala31Thr | missense_variant | 1.0 | linezolid | Uncertain significance |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.99 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 1.0 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.99 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 1.0 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1471842 | n.-4T>G | upstream_gene_variant | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
rrs | 1472555 | n.710C>T | non_coding_transcript_exon_variant | 0.97 | streptomycin | Uncertain significance |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.99 | linezolid | Not assoc w R |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
bacA | 2062922 | p.Ile603Val | missense_variant | 1.0 | streptomycin | Not assoc w R |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2062991 | p.Ala580Thr | missense_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
bacA | 2064885 | c.-157G>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
ndh | 2102045 | c.997delG | frameshift_variant | 1.0 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.99 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 | isoniazid | |
Rv2477c | 2784139 | c.-98delC | upstream_gene_variant | 1.0 | ethambutol | |
moxifloxacin | ||||||
streptomycin | ||||||
levofloxacin | ||||||
kanamycin | ||||||
rifampicin | ||||||
amikacin | ||||||
Rv2680 | 2995801 | c.-304C>A | upstream_gene_variant | 1.0 | capreomycin | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 1.0 | ethionamide | Uncertain significance |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.99 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
clpC1 | 4040517 | p.Val63Ala | missense_variant | 1.0 | pyrazinamide | Not assoc w R - Interim |
glpK | 4138377 | p.Val460Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embC | 4240671 | p.Thr270Ile | missense_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4240750 | c.888C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4241042 | p.Asn394Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4246870 | c.357C>T | synonymous_variant | 1.0 | ethambutol | |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 1.0 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 | ethionamide | Uncertain significance |
ethA | 4327450 | c.24C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.99 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 1.0 | streptomycin | Not assoc w R |