Run ID: ERR4827935
Sample name:
Date: 2024-10-05T08:40:37.630003
Number of reads: 4253996
Percentage reads mapped: 99.36
Median coverage: 127.0
Strain: lineage2.2.1;lineage5
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.36 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.4 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.3 |
lineage5 | West-Africa 1 | RD711 | 0.48 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
p.Glu761Asp | Uncertain significance | Mutation from literature | ||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Asp354Ala | Assoc w R | |
pyrazinamide | ||||
streptomycin | rrs | n.517C>T | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-37G>T | Assoc w R | |
cycloserine | ||||
ethionamide | ethA | c.-7T>C | Assoc w R - Interim | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.24 | rifampicin | Assoc w R | |
rpoB | 762089 | p.Glu761Asp | missense_variant | 0.35 | rifampicin | Uncertain significance | Mutation from literature |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.34 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.31 | isoniazid | Assoc w R | High-level resistance |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 0.51 | kanamycin | Assoc w R | |
embB | 4247574 | p.Asp354Ala | missense_variant | 0.38 | ethambutol | Assoc w R | |
ethA | 4327480 | c.-7T>C | upstream_gene_variant | 0.32 | ethionamide | Assoc w R - Interim |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 36 | c.36G>A | synonymous_variant | 0.85 | isoniazid | |
gyrB | 6446 | p.Ala403Ser | missense_variant | 0.87 | levofloxacin | Not assoc w R |
moxifloxacin | Uncertain significance | |||||
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 | 9143 | c.1842T>C | synonymous_variant | 0.86 | 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 | |||||
gyrA | 9566 | c.2265C>T | synonymous_variant | 0.68 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
Rv0010c | 13460 | c.99T>C | synonymous_variant | 0.7 | 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 | 575907 | p.Ala187Val | missense_variant | 0.43 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.31 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.26 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.2 | ethionamide | Uncertain significance |
Rv0565c | 657578 | c.-108T>C | upstream_gene_variant | 0.79 | ethionamide | |
rpoB | 763031 | c.3225T>C | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 766645 | p.Glu1092Asp | 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 | 0.2 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.43 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1253750 | p.Asp262Gly | missense_variant | 0.89 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
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 | |||||
fbiC | 1302899 | c.-32A>G | upstream_gene_variant | 0.53 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
sigE | 1364706 | c.294G>A | synonymous_variant | 0.31 | pyrazinamide | Not assoc w R - Interim |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.45 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embR | 1417554 | c.-207C>G | upstream_gene_variant | 0.66 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.24 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1853565 | c.-41G>A | upstream_gene_variant | 0.55 | linezolid | Uncertain significance |
tsnR | 1854247 | c.642A>G | synonymous_variant | 0.45 | 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 | 0.57 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ndh | 2101921 | c.1122G>A | synonymous_variant | 0.67 | isoniazid | Not assoc w R - Interim |
delamanid | Not assoc w R - Interim | |||||
ethionamide | Not assoc w R - Interim | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 1.0 | isoniazid | Not assoc w R |
katG | 2155947 | c.165T>G | synonymous_variant | 0.47 | isoniazid | |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 1.0 | pyrazinamide | 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 | |||||
pncA | 2289226 | p.Ile6Leu | missense_variant | 0.33 | pyrazinamide | Not assoc w R - Interim |
kasA | 2518132 | c.18C>T | synonymous_variant | 0.77 | isoniazid | |
folC | 2747433 | c.166C>T | synonymous_variant | 0.8 | para-aminosalicylic_acid | |
pepQ | 2860154 | c.256_264delCGGGCCGGC | conservative_inframe_deletion | 0.51 | bedaquiline | |
clofazimine | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3087084 | c.266delA | frameshift_variant | 0.45 | cycloserine | |
Rv3083 | 3449022 | c.519C>T | synonymous_variant | 0.81 | ethionamide | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.24 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3624350 | c.561G>T | synonymous_variant | 0.52 | rifampicin | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
lpqB | 3624486 | p.Asp142Gly | missense_variant | 0.61 | 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 | 3626562 | p.Pro18Ser | missense_variant | 0.35 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrA | 3627920 | c.-571A>C | upstream_gene_variant | 0.54 | rifampicin | |
bedaquiline | ||||||
alr | 3840932 | c.489C>T | synonymous_variant | 0.42 | cycloserine | |
ddn | 3986987 | c.144G>T | synonymous_variant | 0.68 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
glpK | 4138377 | p.Val460Ala | missense_variant | 0.58 | 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 | |||||
glpK | 4139131 | p.Glu209Lys | missense_variant | 0.72 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Not assoc w R | |||||
ethambutol | Uncertain significance | |||||
embC | 4239515 | c.-348C>T | upstream_gene_variant | 0.58 | ethambutol | |
embC | 4239843 | c.-20A>C | upstream_gene_variant | 0.72 | ethambutol | Not assoc w R - Interim |
embC | 4240671 | p.Thr270Ile | missense_variant | 0.52 | 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 | 0.4 | ethambutol | Not assoc w R |
embA | 4244220 | c.988C>T | synonymous_variant | 0.5 | ethambutol | Not assoc w R |
embB | 4247646 | p.Glu378Ala | missense_variant | 0.58 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.45 | ethambutol | Not assoc w R |
ubiA | 4269387 | p.Glu149Asp | missense_variant | 0.75 | ethambutol | Not assoc w R |
ubiA | 4269606 | c.228T>C | synonymous_variant | 0.72 | ethambutol | Not assoc w R |
whiB6 | 4338563 | c.-42G>T | upstream_gene_variant | 0.44 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
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 | 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 | 4407684 | p.Glu173Asp | missense_variant | 0.83 | streptomycin | |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.22 | streptomycin | Not assoc w R |