Run ID: ERR4798336
Sample name:
Date: 2024-04-15T06:53:04.354927
Number of reads: 3388398
Percentage reads mapped: 99.4
Median coverage: 97.0
Strain: lineage1.2.2.2;lineage3
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.45 |
lineage1.2.2 | Indo-Oceanic | RD239 | 0.53 |
lineage1.2.2.2 | Indo-Oceanic | RD239 | 0.52 |
lineage1 | Indo-Oceanic | RD239 | 0.53 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Tyr | Assoc w R | |
p.Ser450Leu | Assoc w R | |||
isoniazid | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Met306Leu | Assoc w R | |
p.Gln497Arg | Assoc w R | |||
pyrazinamide | pncA | p.Ala143Pro | Mutation from literature | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrB | p.Thr500Asn | Uncertain significance | Mutation from literature |
gyrA | p.Ser91Pro | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |
ofloxacin | ||||
levofloxacin | gyrB | p.Thr500Asn | Uncertain significance | Mutation from literature |
gyrA | p.Ser91Pro | Assoc w R | ||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-779G>T | Assoc w R - Interim | Alias fabG1_c.-17G>T |
ethA | p.Pro378Leu | Uncertain significance | Mutation from literature | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrB | 6738 | p.Thr500Asn | missense_variant | 0.58 | levofloxacin | Uncertain significance | Mutation from literature |
moxifloxacin | Uncertain significance | Mutation from literature | |||||
gyrA | 7572 | p.Ser91Pro | missense_variant | 0.5 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
rpoB | 761109 | p.Asp435Tyr | missense_variant | 0.71 | rifampicin | Assoc w R | |
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.28 | rifampicin | Assoc w R | |
inhA | 1673423 | c.-779G>T | upstream_gene_variant | 0.49 | ethionamide | Assoc w R - Interim | Alias fabG1_c.-17G>T |
isoniazid | Assoc w R - Interim | Alias fabG1_c.-17G>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288815 | p.Ala143Pro | missense_variant | 0.47 | pyrazinamide | Mutation from literature | |
embB | 4247429 | p.Met306Leu | missense_variant | 0.49 | ethambutol | Assoc w R | |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.49 | ethambutol | Assoc w R | |
ethA | 4326341 | p.Pro378Leu | missense_variant | 0.48 | ethionamide | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 0.47 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6112 | p.Met291Ile | missense_variant | 0.51 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7268 | c.-34C>T | upstream_gene_variant | 0.5 | 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 | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8452 | p.Ala384Val | missense_variant | 0.45 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.44 | 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 | 0.44 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.47 | isoniazid | Not assoc w R |
Rv0010c | 13699 | c.-141A>G | upstream_gene_variant | 0.47 | isoniazid | Not assoc w R |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.52 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.38 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.5 | rifampicin | Not assoc w R |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.44 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.54 | 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 | 0.47 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.47 | 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 | 0.59 | linezolid | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | 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 | 0.54 | ethambutol | Not assoc w R |
embR | 1417040 | p.Leu103Pro | missense_variant | 0.46 | ethambutol | Uncertain significance |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.57 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.55 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473021 | n.1176G>A | non_coding_transcript_exon_variant | 0.62 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.45 | 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 |
tlyA | 1918719 | c.780G>A | synonymous_variant | 0.37 | capreomycin | |
bacA | 2062922 | p.Ile603Val | missense_variant | 0.59 | streptomycin | Not assoc w R |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2064372 | c.357A>G | synonymous_variant | 0.42 | streptomycin | Not assoc w R - Interim |
kanamycin | Not assoc w R - Interim | |||||
capreomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R - Interim | |||||
ndh | 2102240 | p.Arg268His | missense_variant | 0.51 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Not assoc w R - Interim | |||||
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 |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.6 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.44 | 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 | |||||
Rv1979c | 2223553 | c.-389C>A | upstream_gene_variant | 0.61 | clofazimine | Not assoc w R |
bedaquiline | Uncertain significance | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 0.54 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.52 | pyrazinamide | |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.47 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.63 | isoniazid | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.45 | isoniazid | Not assoc w R |
ahpC | 2726418 | p.Glu76Lys | missense_variant | 0.53 | isoniazid | Uncertain significance |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.44 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.48 | ethionamide | Uncertain significance |
Rv3236c | 3612109 | p.Phe336Leu | missense_variant | 0.53 | pyrazinamide | Uncertain significance |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.54 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626467 | c.147G>A | synonymous_variant | 0.51 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R | |||||
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.5 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040719 | c.-15A>G | upstream_gene_variant | 0.57 | pyrazinamide | Uncertain significance |
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.41 | pyrazinamide | |
glpK | 4138377 | p.Val460Ala | missense_variant | 0.47 | 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 | |||||
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.41 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embC | 4240671 | p.Thr270Ile | missense_variant | 0.49 | ethambutol | Not assoc w R |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.51 | ethambutol | Not assoc w R |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.44 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243228 | c.-5G>A | upstream_gene_variant | 0.44 | ethambutol | Uncertain significance |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.54 | ethambutol | Not assoc w R |
embB | 4246430 | c.-84C>T | upstream_gene_variant | 0.52 | ethambutol | |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.52 | ethambutol | Not assoc w R |
aftB | 4267960 | p.Val293Met | missense_variant | 0.53 | ethambutol | Uncertain significance |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.55 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.56 | ethambutol | Not assoc w R |
ethA | 4326148 | c.1326G>T | synonymous_variant | 0.53 | ethionamide | Not assoc w R - Interim |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.52 | ethionamide | Uncertain significance |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.59 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
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 | 0.54 | 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 | 4407848 | p.Ala119Thr | missense_variant | 0.48 | streptomycin | Uncertain significance |
gid | 4407873 | c.330G>T | synonymous_variant | 0.5 | streptomycin | Not assoc w R |
gid | 4408060 | p.His48Pro | missense_variant | 0.48 | streptomycin | Uncertain significance |
gid | 4408072 | p.Leu44Pro | missense_variant | 0.53 | streptomycin | Uncertain significance |