Run ID: ERR4796347
Sample name:
Date: 2024-04-15T21:19:56.624267
Number of reads: 3658273
Percentage reads mapped: 99.39
Median coverage: 105.0
Strain: lineage1.2.2.2;lineage2.2.1;lineage3.1.2.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.07 |
lineage1.2.2 | Indo-Oceanic | RD239 | 0.73 |
lineage3.1.2 | East-African-Indian | RD750 | 0.06 |
lineage2 | East-Asian | RD105 | 0.17 |
lineage1.2.2.2 | Indo-Oceanic | RD239 | 0.7 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.19 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.18 |
lineage1 | Indo-Oceanic | RD239 | 0.72 |
lineage3.1.2.1 | East-African-Indian | RD750 | 0.08 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | 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) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Gln497Arg | Assoc w R | |
pyrazinamide | pncA | p.Gly132Ala | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
kanamycin | rrs | n.1401A>G | Assoc w R | |
eis | c.-10G>C | Uncertain significance | Mutation from literature | |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.16 | 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 | 761155 | p.Ser450Leu | missense_variant | 0.23 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.17 | streptomycin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.36 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.22 | 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) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.17 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288847 | p.Gly132Ala | missense_variant | 0.24 | pyrazinamide | Assoc w R | |
eis | 2715342 | c.-10G>C | upstream_gene_variant | 0.22 | kanamycin | Uncertain significance | Mutation from literature |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.12 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 0.71 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 6112 | p.Met291Ile | missense_variant | 0.76 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7268 | c.-34C>T | upstream_gene_variant | 0.61 | 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 | 7773 | p.Gly158Ser | missense_variant | 0.77 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
gyrA | 8452 | p.Ala384Val | missense_variant | 0.75 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.67 | 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 | 0.76 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.62 | isoniazid | Not assoc w R |
Rv0010c | 13699 | c.-141A>G | upstream_gene_variant | 0.7 | isoniazid | Not assoc w R |
fgd1 | 491290 | p.Val170Met | missense_variant | 0.23 | clofazimine | Not assoc w R |
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 | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.14 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
mshA | 576108 | p.Ala254Gly | missense_variant | 0.27 | ethionamide | |
isoniazid | ||||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.23 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.26 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.72 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.76 | 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 | 0.69 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.69 | 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 | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.17 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.22 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 0.67 | linezolid | Not assoc w R |
Rv1129c | 1253278 | c.1257C>T | synonymous_variant | 0.11 | moxifloxacin | |
levofloxacin | ||||||
rifampicin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
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 | 0.61 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.7 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.71 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.23 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.7 | 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 | 0.77 | streptomycin | Not assoc w R |
kanamycin | Not assoc w R | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ndh | 2102240 | p.Arg268His | missense_variant | 0.73 | 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 |
katG | 2156355 | c.-244C>T | upstream_gene_variant | 0.81 | isoniazid | Uncertain significance |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 0.73 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.74 | 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 | 0.77 | clofazimine | Not assoc w R |
bedaquiline | Uncertain significance | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.68 | isoniazid | |
eis | 2714401 | p.Ala311Val | missense_variant | 0.13 | amikacin | |
kanamycin | ||||||
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.65 | isoniazid | |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.18 | 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 | 0.76 | ethionamide | Uncertain significance |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.2 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.7 | 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 | 0.65 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.25 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
rpoA | 3877750 | p.Asp253Gly | missense_variant | 0.24 | rifampicin | Uncertain significance |
rpoA | 3878312 | p.Val66Leu | missense_variant | 0.72 | rifampicin | Uncertain significance |
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.66 | pyrazinamide | Not assoc w R - Interim |
clpC1 | 4040719 | c.-15A>G | upstream_gene_variant | 0.77 | pyrazinamide | Uncertain significance |
glpK | 4138377 | p.Val460Ala | missense_variant | 0.75 | 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 | 0.76 | ethambutol | Not assoc w R |
embC | 4241022 | p.Ala387Val | missense_variant | 0.23 | ethambutol | Uncertain significance |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.75 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.19 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.71 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.71 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.21 | ethambutol | Not assoc w R |
aftB | 4267960 | p.Val293Met | missense_variant | 0.66 | ethambutol | Uncertain significance |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.68 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.78 | ethambutol | Not assoc w R |
ethA | 4326148 | c.1326G>T | synonymous_variant | 0.76 | ethionamide | Not assoc w R - Interim |
ethA | 4326439 | p.Asn345Lys | missense_variant | 0.77 | ethionamide | Uncertain significance |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 0.69 | 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 | 0.66 | 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 | 4407620 | p.Tyr195His | missense_variant | 0.23 | streptomycin | Not assoc w R |
gid | 4407724 | p.Leu160Arg | missense_variant | 0.13 | streptomycin | Uncertain significance |
gid | 4407848 | p.Ala119Thr | missense_variant | 0.72 | streptomycin | Uncertain significance |
gid | 4407873 | c.330G>T | synonymous_variant | 0.71 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.13 | streptomycin | Not assoc w R |