Run ID: SRR19573671
Sample name:
Date: 2024-10-04T02:30:52.594164
Number of reads: 15116906
Percentage reads mapped: 98.05
Median coverage: 175.5
Strain: lineage1.2.2.2
Spoligotype:
Drug-resistance: Other
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.2.2 | Indo-Oceanic | RD239 | 0.99 |
lineage1.2.2.2 | Indo-Oceanic | RD239 | 1.0 |
lineage1 | Indo-Oceanic | RD239 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | ||||
ethambutol | embB | p.Gln497Arg | Assoc w R | |
pyrazinamide | ||||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
embB | 4248003 | p.Gln497Arg | missense_variant | 0.33 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5075 | c.-165C>T | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
gyrB | 5078 | c.-162_-161insG | 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 | 7268 | c.-34C>T | upstream_gene_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 | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8452 | p.Ala384Val | missense_variant | 0.99 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
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 | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.99 | isoniazid | Not assoc w R |
Rv0010c | 13482 | p.Ala26Val | missense_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13548 | p.Thr4Ile | missense_variant | 1.0 | isoniazid | Not assoc w R |
Rv0010c | 13699 | c.-141A>G | upstream_gene_variant | 0.82 | isoniazid | Not assoc w R |
fgd1 | 491742 | c.960T>C | synonymous_variant | 1.0 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 575092 | c.-256C>A | upstream_gene_variant | 0.17 | isoniazid | |
ethionamide | ||||||
mshA | 575121 | c.-227G>C | upstream_gene_variant | 0.2 | isoniazid | |
ethionamide | ||||||
mshA | 575265 | c.-83C>A | upstream_gene_variant | 0.27 | isoniazid | |
ethionamide | ||||||
mshA | 576337 | c.990G>A | synonymous_variant | 0.27 | isoniazid | Not assoc w R - Interim |
ethionamide | Not assoc w R - Interim | |||||
Rv0565c | 656322 | c.1149C>T | synonymous_variant | 0.5 | ethionamide | |
Rv0565c | 656991 | c.480G>A | synonymous_variant | 0.24 | ethionamide | |
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 |
mmaA3 | 737374 | p.Ile259Ser | missense_variant | 0.18 | isoniazid | |
mmaA3 | 737609 | p.Lys181Glu | missense_variant | 0.33 | isoniazid | |
rpoB | 759670 | c.-137C>T | upstream_gene_variant | 0.15 | rifampicin | Uncertain significance |
rpoB | 761012 | p.Asp402Glu | missense_variant | 0.22 | rifampicin | |
rpoB | 761748 | p.Ser648Thr | missense_variant | 0.32 | rifampicin | |
rpoB | 761786 | c.1980C>T | synonymous_variant | 0.99 | rifampicin | Not assoc w R - Interim |
rpoB | 761863 | p.Ala686Val | missense_variant | 0.99 | rifampicin | |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoB | 763321 | p.Ala1172Val | missense_variant | 0.69 | rifampicin | |
rpoC | 763884 | p.Ala172Val | missense_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 764002 | c.633C>T | synonymous_variant | 0.96 | rifampicin | |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 778483 | c.-3C>T | upstream_gene_variant | 0.12 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 | streptomycin | Not assoc w R |
rplC | 800815 | p.Arg3* | stop_gained | 0.27 | linezolid | |
rplC | 800838 | p.Lys10Asn | missense_variant | 0.17 | linezolid | |
Rv1129c | 1253587 | c.948C>T | synonymous_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
Rv1129c | 1254747 | c.-213C>A | upstream_gene_variant | 1.0 | levofloxacin | |
moxifloxacin | ||||||
isoniazid | ||||||
rifampicin | ||||||
fbiC | 1304750 | p.Pro607Leu | missense_variant | 0.72 | pretomanid | |
delamanid | ||||||
clofazimine | ||||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.73 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 1.0 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.89 | ethambutol | |
embR | 1417933 | c.-587_-586insT | upstream_gene_variant | 0.26 | ethambutol | |
embR | 1417933 | c.-586G>T | upstream_gene_variant | 0.64 | ethambutol | |
atpE | 1460975 | c.-70G>A | upstream_gene_variant | 0.2 | bedaquiline | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472138 | n.293C>T | non_coding_transcript_exon_variant | 0.11 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474625 | n.968T>G | non_coding_transcript_exon_variant | 0.37 | capreomycin | |
linezolid | ||||||
rrl | 1474711 | n.1054_1055insC | non_coding_transcript_exon_variant | 0.22 | capreomycin | |
linezolid | ||||||
rrl | 1475601 | n.1944C>T | non_coding_transcript_exon_variant | 0.15 | capreomycin | |
linezolid | ||||||
tsnR | 1853763 | p.Ala53Val | missense_variant | 0.57 | linezolid | Uncertain significance |
tsnR | 1853974 | c.369C>T | synonymous_variant | 1.0 | linezolid | Not assoc w R |
tsnR | 1854038 | p.Asp145Asn | missense_variant | 0.44 | linezolid | |
tsnR | 1854144 | p.Ala180Val | missense_variant | 0.29 | linezolid | |
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 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ndh | 2102078 | p.Asp322Val | missense_variant | 0.22 | isoniazid | |
delamanid | ||||||
ethionamide | ||||||
ndh | 2102242 | c.801G>A | synonymous_variant | 0.71 | isoniazid | |
delamanid | ||||||
ethionamide | ||||||
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
katG | 2155668 | c.444G>A | synonymous_variant | 0.57 | isoniazid | |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2168742 | p.Gly624Asp | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2222519 | p.Gly216Ser | missense_variant | 0.85 | bedaquiline | |
clofazimine | ||||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223553 | c.-389C>A | upstream_gene_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Not assoc w R | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 1.0 | isoniazid | |
eis | 2715261 | c.72C>T | synonymous_variant | 0.23 | kanamycin | |
amikacin | ||||||
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 1.0 | isoniazid | |
ahpC | 2726693 | c.501C>T | synonymous_variant | 0.36 | isoniazid | |
folC | 2746509 | p.Gln364* | stop_gained | 0.45 | para-aminosalicylic_acid | |
folC | 2747542 | c.57C>T | synonymous_variant | 0.89 | para-aminosalicylic_acid | |
Rv2477c | 2783487 | p.Pro186Ala | missense_variant | 0.21 | kanamycin | |
levofloxacin | ||||||
moxifloxacin | ||||||
streptomycin | ||||||
rifampicin | ||||||
ethambutol | ||||||
amikacin | ||||||
pepQ | 2859323 | p.Pro366Ser | missense_variant | 0.25 | bedaquiline | |
clofazimine | ||||||
Rv2681 | 2997883 | p.Cys382Tyr | missense_variant | 0.75 | capreomycin | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086953 | p.Ile45Thr | missense_variant | 0.35 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.96 | ethionamide | Uncertain significance |
whiB7 | 3568821 | c.-142A>C | upstream_gene_variant | 0.2 | kanamycin | |
amikacin | ||||||
streptomycin | ||||||
lpqB | 3623551 | p.Arg454Cys | missense_variant | 0.36 | rifampicin | |
bedaquiline | ||||||
lpqB | 3624486 | p.Asp142Gly | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
lpqB | 3625492 | c.-582C>T | upstream_gene_variant | 0.2 | rifampicin | |
bedaquiline | ||||||
lpqB | 3625587 | c.-677C>T | upstream_gene_variant | 0.46 | rifampicin | |
bedaquiline | ||||||
mtrB | 3626467 | c.147G>A | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpoA | 3878817 | c.-310T>A | upstream_gene_variant | 1.0 | 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 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
embC | 4240276 | c.414G>A | synonymous_variant | 0.78 | ethambutol | |
embC | 4240671 | p.Thr270Ile | missense_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 |
embA | 4246312 | p.Gly1027Ala | missense_variant | 0.21 | ethambutol | |
embA | 4246314 | p.Gly1028Arg | missense_variant | 0.38 | ethambutol | |
embA | 4246359 | p.Ala1043Thr | missense_variant | 0.21 | ethambutol | |
embB | 4247512 | c.999T>C | synonymous_variant | 0.24 | ethambutol | |
embB | 4247646 | p.Glu378Ala | missense_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4247889 | p.Gly459Asp | missense_variant | 0.28 | ethambutol | |
aftB | 4267055 | c.1782C>T | synonymous_variant | 0.62 | ethambutol | |
aftB | 4267472 | c.1365C>G | synonymous_variant | 0.19 | ethambutol | |
aftB | 4268560 | p.Leu93Met | missense_variant | 0.48 | ethambutol | |
ubiA | 4269606 | c.228T>C | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4326019 | c.1455C>T | synonymous_variant | 0.32 | ethionamide | Not assoc w R - Interim |
ethA | 4326148 | c.1326G>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
ethA | 4326439 | p.Asn345Lys | missense_variant | 1.0 | ethionamide | Uncertain significance |
ethR | 4327828 | p.Pro94Ser | missense_variant | 0.79 | ethionamide | Uncertain significance |
whiB6 | 4338203 | p.Arg107Cys | missense_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 1.0 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 0.96 | streptomycin | Not assoc w R |
gid | 4408013 | p.Arg64Trp | missense_variant | 0.93 | streptomycin | Uncertain significance |