Run ID: ERR10748114
Sample name:
Date: 2024-04-15T06:22:23.443169
Number of reads: 1537807
Percentage reads mapped: 99.92
Median coverage: 80.0
Strain: lineage2.2.1;lineage4.8.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.3 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.27 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.25 |
lineage4 | Euro-American | None | 0.72 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.72 |
lineage4.8.1 | Euro-American (mainly T) | RD219 | 0.73 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | p.Thr160Ala | Not assoc w R - Interim | Mutation from literature |
p.Thr100Ile | Uncertain significance | Mutation from literature | ||
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | p.Gly43Cys | Uncertain significance | Mutation from literature |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.41 | moxifloxacin | Assoc w R | High-level resistance |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.23 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.3 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288764 | p.Thr160Ala | missense_variant | 0.42 | pyrazinamide | Not assoc w R - Interim | Mutation from literature |
pncA | 2288943 | p.Thr100Ile | missense_variant | 0.4 | pyrazinamide | Uncertain significance | Mutation from literature |
embB | 4247431 | p.Met306Ile | missense_variant | 0.28 | ethambutol | Assoc w R | |
ethA | 4327347 | p.Gly43Cys | missense_variant | 0.34 | ethionamide | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrA | 7114 | c.-188C>G | upstream_gene_variant | 0.67 | levofloxacin | |
moxifloxacin | ||||||
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 0.37 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.51 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491328 | c.546C>G | synonymous_variant | 0.37 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
fgd1 | 491330 | p.Lys183Met | missense_variant | 0.36 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.3 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.28 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.39 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.45 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.45 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.23 | rifampicin | Not assoc w R |
rpoC | 764822 | p.Asp485Tyr | missense_variant | 0.23 | rifampicin | Uncertain significance |
mmpL5 | 775592 | c.2889G>A | synonymous_variant | 0.21 | clofazimine | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
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 | 0.28 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.3 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.24 | 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 | 0.19 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.36 | 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 | 0.64 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rpsA | 1833288 | c.-254T>C | upstream_gene_variant | 0.75 | pyrazinamide | |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.24 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.17 | 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 | 0.31 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.26 | pyrazinamide | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.68 | pyrazinamide | Not assoc w R |
PPE35 | 2170892 | c.-280G>A | upstream_gene_variant | 0.65 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.72 | capreomycin | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.32 | cycloserine | |
fbiD | 3339040 | c.-78T>C | upstream_gene_variant | 0.59 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
Rv3083 | 3449315 | p.Trp271* | stop_gained | 1.0 | ethionamide | Uncertain significance |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.35 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.34 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.18 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiB | 3642874 | p.Leu447Arg | missense_variant | 0.74 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.25 | ethambutol | Not assoc w R |
embB | 4247717 | p.Leu402Val | missense_variant | 0.37 | ethambutol | Uncertain significance |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.14 | ethambutol | Not assoc w R |
whiB6 | 4338365 | p.Cys53Arg | missense_variant | 0.21 | capreomycin | Uncertain significance |
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 | 0.21 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.31 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.37 | streptomycin | Not assoc w R |