Run ID: ERR4797622
Sample name:
Date: 2024-10-03T15:30:57.881431
Number of reads: 4409302
Percentage reads mapped: 99.5
Median coverage: 136.0
Strain: lineage1.1.2;lineage2.2.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage1.1.2 | Indo-Oceanic | RD239 | 0.29 |
lineage2 | East-Asian | RD105 | 0.72 |
lineage1.1 | Indo-Oceanic | RD239 | 0.3 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.69 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.73 |
lineage1 | Indo-Oceanic | RD239 | 0.28 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
rpoC | p.Ile491Thr | Uncertain significance | Mutation from literature | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embA | c.-16C>T | Uncertain significance | Mutation from literature |
pyrazinamide | pncA | p.Ile5Ser | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Asn | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Asn | 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.-12C>T | Assoc w R | ||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | thyA | p.Thr22Ala | Mutation from literature | |
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Asn | missense_variant | 0.6 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.67 | rifampicin | Assoc w R | |
rpoC | 764841 | p.Ile491Thr | missense_variant | 0.69 | rifampicin | Uncertain significance | Mutation from literature |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.78 | streptomycin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.6 | amikacin | Assoc w R | |
capreomycin | Assoc w R | ||||||
kanamycin | Assoc w R | ||||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.7 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289228 | p.Ile5Ser | missense_variant | 0.75 | pyrazinamide | Assoc w R | |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 0.68 | kanamycin | Assoc w R | |
thyA | 3074408 | p.Thr22Ala | missense_variant | 0.68 | para-aminosalicylic_acid | Mutation from literature | |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.77 | ethambutol | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6112 | p.Met291Ile | missense_variant | 0.34 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrB | 6124 | c.885C>T | synonymous_variant | 0.36 | 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 | 0.31 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9143 | c.1842T>C | synonymous_variant | 0.26 | 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 | 0.27 | isoniazid | Not assoc w R |
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.25 | isoniazid | Not assoc w R |
fgd1 | 491290 | p.Val170Met | missense_variant | 0.67 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | 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 | 575646 | c.301delG | frameshift_variant | 0.7 | isoniazid | Uncertain significance |
ethionamide | Uncertain significance | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.73 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.71 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.65 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.75 | ethionamide | Uncertain significance |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.24 | ethionamide | |
nusG | 734116 | c.-138T>C | upstream_gene_variant | 0.28 | 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 | 0.31 | rifampicin | Not assoc w R |
rpoC | 763886 | c.517C>A | synonymous_variant | 0.31 | rifampicin | Not assoc w R |
rpoC | 765171 | p.Pro601Leu | missense_variant | 0.27 | rifampicin | Not assoc w R |
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 | 776182 | p.Asp767Asn | missense_variant | 0.68 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpR5 | 779216 | p.Gln76Arg | missense_variant | 0.8 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.66 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.99 | streptomycin | Not assoc w R |
rplC | 800357 | c.-452C>A | upstream_gene_variant | 0.29 | linezolid | Not assoc w R |
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 | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.74 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embR | 1417019 | p.Cys110Tyr | missense_variant | 0.32 | ethambutol | Not assoc w R |
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.34 | ethambutol | |
embR | 1417793 | c.-446C>T | upstream_gene_variant | 0.31 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472873 | n.1028C>A | non_coding_transcript_exon_variant | 0.34 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
streptomycin | ||||||
amikacin | Uncertain significance | |||||
rrl | 1475479 | n.1822C>T | non_coding_transcript_exon_variant | 0.68 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.69 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1853974 | c.369C>T | synonymous_variant | 0.25 | linezolid | Not assoc w R |
tsnR | 1854045 | p.Tyr147Cys | missense_variant | 0.23 | 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 | 0.17 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
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 | 2167983 | p.Gly877Asp | missense_variant | 0.29 | pyrazinamide | Uncertain significance |
Rv1979c | 2222308 | p.Asp286Gly | missense_variant | 0.25 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2518132 | c.18C>T | synonymous_variant | 0.24 | isoniazid | |
ahpC | 2726051 | c.-142G>A | upstream_gene_variant | 0.28 | isoniazid | |
Rv2681 | 2996912 | c.174C>T | synonymous_variant | 0.31 | capreomycin | Not assoc w R |
Rv2752c | 3064632 | c.1560C>T | synonymous_variant | 0.25 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Not assoc w R | |||||
thyX | 3067949 | c.-4C>T | upstream_gene_variant | 0.71 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448714 | p.Asp71His | missense_variant | 0.24 | ethionamide | Uncertain significance |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.64 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.22 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626481 | c.133C>T | synonymous_variant | 0.29 | rifampicin | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.67 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4040517 | p.Val63Ala | missense_variant | 0.39 | pyrazinamide | Not assoc w R - Interim |
glpK | 4138377 | p.Val460Ala | missense_variant | 0.23 | 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 | 4240671 | p.Thr270Ile | missense_variant | 0.34 | ethambutol | Not assoc w R |
embC | 4241022 | p.Ala387Val | missense_variant | 0.7 | ethambutol | Uncertain significance |
embC | 4241042 | p.Asn394Asp | missense_variant | 0.31 | 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 | 0.65 | ethambutol | Not assoc w R |
embA | 4243848 | p.Val206Met | missense_variant | 0.33 | ethambutol | Not assoc w R |
embA | 4245969 | p.Pro913Ser | missense_variant | 0.26 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.37 | ethambutol | Not assoc w R |
embB | 4247847 | p.Gln445Arg | missense_variant | 0.66 | ethambutol | Uncertain significance |
embB | 4249673 | p.Ser1054Pro | missense_variant | 0.3 | ethambutol | Not assoc w R - Interim |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.69 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.32 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.28 | ethambutol | Not assoc w R |
ethA | 4326977 | p.His166Pro | missense_variant | 0.7 | ethionamide | Uncertain significance |
whiB6 | 4338292 | p.Ala77Val | missense_variant | 0.75 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338603 | c.-82C>T | upstream_gene_variant | 0.23 | 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 | 4407620 | p.Tyr195His | missense_variant | 0.75 | streptomycin | Not assoc w R |
gid | 4407873 | c.330G>T | synonymous_variant | 0.24 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.66 | streptomycin | Not assoc w R |