Run ID: ERR133972
Sample name:
Date: 2024-04-15T18:19:08.867021
Number of reads: 9717674
Percentage reads mapped: 99.62
Median coverage: 212.0
Strain: lineage2.2.1;lineage4.8
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.51 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.5 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.5 |
lineage4 | Euro-American | None | 0.53 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.51 |
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 | rpsL | p.Lys88Arg | Assoc w R | |
rrs | n.517C>T | Assoc w R | ||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
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.754_755dupGC | 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 |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin | Assoc w R | |
rpoB | 762089 | p.Glu761Asp | missense_variant | 0.52 | rifampicin | Uncertain significance | Mutation from literature |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.49 | streptomycin | Assoc w R | |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.5 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.51 | isoniazid | Assoc w R | High-level resistance |
eis | 2715342 | c.-10G>A | upstream_gene_variant | 0.49 | kanamycin | Assoc w R | Can only confer resistance if genetically linked to a functional Eis |
eis | 2715369 | c.-37G>T | upstream_gene_variant | 0.51 | kanamycin | Assoc w R | |
embB | 4247574 | p.Asp354Ala | missense_variant | 0.5 | ethambutol | Assoc w R | |
ethA | 4326718 | c.754_755dupGC | frameshift_variant | 0.45 | ethionamide | Assoc w R | |
ethA | 4327480 | c.-7T>C | upstream_gene_variant | 0.51 | ethionamide | Assoc w R - Interim |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6432 | p.Ala398Val | missense_variant | 0.47 | levofloxacin | Uncertain significance |
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 | 0.43 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.52 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.55 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.5 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.55 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.44 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.44 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.57 | rifampicin | Not assoc w R |
rpoC | 764916 | p.Leu516Pro | missense_variant | 0.48 | rifampicin | Uncertain significance |
rpoC | 766645 | p.Glu1092Asp | missense_variant | 0.47 | 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 | 0.5 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.51 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.46 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.48 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
sigE | 1364706 | c.294G>A | synonymous_variant | 0.5 | pyrazinamide | Not assoc w R - Interim |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.42 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.54 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.53 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.56 | 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 | 0.49 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.55 | pyrazinamide | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.53 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2289226 | p.Ile6Leu | missense_variant | 0.55 | pyrazinamide | Not assoc w R - Interim |
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.57 | capreomycin | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.52 | cycloserine | |
Rv3083 | 3448383 | c.-121T>C | upstream_gene_variant | 0.5 | ethionamide | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.43 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.49 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.52 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiB | 3642793 | p.Pro420Leu | missense_variant | 0.47 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.48 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.43 | ethambutol | Not assoc w R |
whiB6 | 4338563 | c.-42G>T | upstream_gene_variant | 0.5 | capreomycin | Not assoc w R |
amikacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
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 | 4338732 | c.-211C>T | upstream_gene_variant | 0.51 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.52 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.5 | streptomycin | Not assoc w R |