Run ID: ERR403282
Sample name:
Date: 2024-10-04T12:51:28.620221
Number of reads: 3817087
Percentage reads mapped: 99.62
Median coverage: 88.0
Strain: lineage2.2.1;lineage4.3.3
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.21 |
lineage2 | East-Asian | RD105 | 0.83 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.81 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.81 |
lineage4 | Euro-American | None | 0.18 |
lineage4.3.3 | Euro-American (LAM) | RD115 | 0.19 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
p.Glu761Asp | Uncertain significance | Mutation from literature | ||
rpoC | p.Ile491Thr | Uncertain significance | Mutation from literature | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Val | Assoc w R | |
p.Asp354Ala | Assoc w R | |||
pyrazinamide | pncA | p.Trp119Arg | Assoc w R - Interim | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
rrs | n.517C>T | Assoc w R | ||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-10G>A | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
c.-37G>T | Assoc w R | |||
cycloserine | ||||
ethionamide | ethA | c.1010delT | Assoc w R | |
c.-7T>C | Assoc w R - Interim | |||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.47 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.88 | rifampicin | Assoc w R | |
rpoB | 762089 | p.Glu761Asp | missense_variant | 0.18 | rifampicin | Uncertain significance | Mutation from literature |
rpoC | 764841 | p.Ile491Thr | missense_variant | 0.57 | rifampicin | Uncertain significance | Mutation from literature |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.75 | streptomycin | Assoc w R | |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.19 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.79 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288887 | p.Trp119Arg | missense_variant | 0.58 | pyrazinamide | Assoc w R - Interim | |
eis | 2715342 | c.-10G>A | upstream_gene_variant | 0.67 | kanamycin | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 0.14 | kanamycin | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 0.67 | ethambutol | Assoc w R | |
embB | 4247574 | p.Asp354Ala | missense_variant | 0.21 | ethambutol | Assoc w R | |
ethA | 4326463 | c.1010delT | frameshift_variant | 0.62 | ethionamide | Assoc w R | |
ethA | 4327480 | c.-7T>C | upstream_gene_variant | 0.15 | ethionamide | Assoc w R - Interim |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
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 | 8040 | p.Gly247Ser | missense_variant | 0.13 | 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 | 13471 | p.Leu30Val | missense_variant | 0.22 | isoniazid | Uncertain significance |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.83 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.83 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.84 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.77 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.81 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.73 | rifampicin | Not assoc w R |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.16 | 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 | 0.82 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.83 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.84 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.89 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
fbiC | 1303095 | c.165G>A | synonymous_variant | 0.21 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
sigE | 1364706 | c.294G>A | synonymous_variant | 0.14 | pyrazinamide | Not assoc w R - Interim |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.74 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.85 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834836 | p.Met432Thr | missense_variant | 0.19 | pyrazinamide | Not assoc w R - Interim |
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 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.79 | isoniazid | Not assoc w R |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 0.2 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.75 | 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 | 0.13 | pyrazinamide | Not assoc w R - Interim |
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.17 | isoniazid | |
ribD | 2986827 | c.-12G>A | upstream_gene_variant | 0.61 | para-aminosalicylic_acid | |
Rv2752c | 3064895 | p.Ala433Ser | missense_variant | 0.56 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.17 | para-aminosalicylic_acid | |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 0.63 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.83 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.82 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.18 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243346 | c.114A>G | synonymous_variant | 0.55 | ethambutol | Not assoc w R - Interim |
embA | 4243460 | c.228C>T | synonymous_variant | 0.83 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.73 | ethambutol | Not assoc w R |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 0.64 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338563 | c.-42G>T | upstream_gene_variant | 0.19 | 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 | 0.83 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.84 | streptomycin | Not assoc w R |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.18 | streptomycin | Not assoc w R |