Run ID: ERR12916918
Sample name:
Date: 2024-05-22T15:48:31.117449
Number of reads: 11398346
Percentage reads mapped: 99.58
Median coverage: 126.0
Strain: lineage2.2.1;lineage4.8
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.58 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.56 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.57 |
lineage4 | Euro-American | None | 0.45 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.46 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
p.Ser315Asn | Assoc w R | High-level resistance | ||
ethambutol | embB | p.Asp354Ala | Assoc w R | |
pyrazinamide | pncA | p.Asp63Ala | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Ala90Val | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ofloxacin | ||||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ddn | p.Trp88* | Assoc w R - Interim | |
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.58 | moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.53 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.51 | isoniazid | Assoc w R | High-level resistance |
katG | 2155168 | p.Ser315Asn | missense_variant | 0.49 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289054 | p.Asp63Ala | missense_variant | 0.55 | pyrazinamide | Assoc w R | |
ddn | 3987106 | p.Trp88* | stop_gained | 0.59 | delamanid | Assoc w R - Interim | |
pretomanid | Assoc w R - Interim | Confers DLM-PMD cross-resistance | |||||
embB | 4247574 | p.Asp354Ala | missense_variant | 0.53 | ethambutol | Assoc w R |
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 | 0.46 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.53 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.58 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.48 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.6 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 656265 | c.1204_1205delAC | frameshift_variant | 0.39 | ethionamide | Uncertain significance |
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.52 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.59 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.61 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.99 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.53 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.62 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpL5 | 778107 | p.Ser125Cys | missense_variant | 0.41 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.56 | 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 | 0.51 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
sigE | 1364202 | c.-211G>A | upstream_gene_variant | 0.44 | pyrazinamide | |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.63 | 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 | 0.38 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.47 | 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 | 0.57 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.61 | pyrazinamide | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.4 | 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 | |||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.39 | capreomycin | |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 0.58 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.63 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.61 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.51 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.55 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
rpoA | 3877956 | p.Glu184Asp | missense_variant | 0.51 | rifampicin | Uncertain significance |
glpK | 4139183 | c.572dupG | frameshift_variant | 0.17 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243346 | c.114A>G | synonymous_variant | 0.52 | ethambutol | Not assoc w R - Interim |
embA | 4243460 | c.228C>T | synonymous_variant | 0.48 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.54 | ethambutol | Not assoc w R |
ethA | 4328378 | c.-905G>C | upstream_gene_variant | 1.0 | ethionamide | |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 0.57 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
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 | 0.54 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.57 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.51 | streptomycin | Not assoc w R |