Run ID: SRR28351240
Sample name:
Date: 2024-05-22T14:57:49.248324
Number of reads: 10626192
Percentage reads mapped: 99.72
Median coverage: 325.0
Strain: lineage2.2.1;lineage4.2.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.39 |
lineage4.2 | Euro-American | None | 0.6 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.41 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.38 |
lineage4 | Euro-American | None | 0.6 |
lineage4.2.1 | Euro-American (TUR) | None | 0.61 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embA | c.-16C>T | Uncertain significance | Mutation from literature |
embB | p.Ser297Ala | Uncertain significance | Mutation from literature | |
p.Met306Ile | Assoc w R | |||
pyrazinamide | pncA | p.His137Arg | Not assoc w R - Interim | Mutation from literature |
p.Phe13Ser | Assoc w R | |||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
p.Lys88Arg | Assoc w R | |||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Tyr | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Tyr | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | eis | c.-12C>T | Assoc w R | |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
ethA | c.884delT | Assoc w R | ||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Tyr | missense_variant | 0.57 | moxifloxacin | Assoc w R | High-level resistance |
levofloxacin | Assoc w R | ||||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.43 | streptomycin | Assoc w R | |
rpsL | 781822 | p.Lys88Arg | missense_variant | 0.61 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.56 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.99 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288832 | p.His137Arg | missense_variant | 0.6 | pyrazinamide | Not assoc w R - Interim | Mutation from literature |
pncA | 2289204 | p.Phe13Ser | missense_variant | 0.4 | pyrazinamide | Assoc w R | |
eis | 2715344 | c.-12C>T | upstream_gene_variant | 0.67 | kanamycin | Assoc w R | |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.57 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247402 | p.Ser297Ala | missense_variant | 0.61 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247431 | p.Met306Ile | missense_variant | 0.42 | ethambutol | Assoc w R | |
ethA | 4326589 | c.884delT | frameshift_variant | 0.33 | ethionamide | 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 | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.99 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491247 | c.465C>T | synonymous_variant | 0.54 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.37 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.36 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 619969 | p.Val27Ile | missense_variant | 0.64 | capreomycin | Not assoc w R - Interim |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.36 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.4 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.37 | ethionamide | Uncertain significance |
rpoB | 761293 | p.Val496Ala | missense_variant | 0.41 | rifampicin | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.46 | rifampicin | Not assoc w R |
rpoC | 764817 | p.Val483Gly | missense_variant | 0.58 | rifampicin | Uncertain significance |
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 | 0.38 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.35 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.37 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 0.58 | linezolid | |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.29 | 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 | 0.35 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.39 | 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 |
bacA | 2063685 | c.1044G>A | synonymous_variant | 0.63 | streptomycin | Not assoc w R - Interim |
kanamycin | Not assoc w R - Interim | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2063911 | p.Ile273Thr | missense_variant | 0.67 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.39 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.32 | pyrazinamide | Not assoc w R |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 0.63 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
ald | 3086731 | c.-89A>G | upstream_gene_variant | 0.34 | cycloserine | |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.66 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.38 | pyrazinamide | Not assoc w R - Interim |
lpqB | 3623222 | c.1689A>G | synonymous_variant | 0.59 | bedaquiline | Not assoc w R - Interim |
rifampicin | Not assoc w R - Interim | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.45 | bedaquiline | Uncertain significance |
rifampicin | 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 | 0.4 | ethambutol | Not assoc w R - Interim |
embA | 4243460 | c.228C>T | synonymous_variant | 0.4 | ethambutol | Not assoc w R |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.62 | ethambutol | Not assoc w R - Interim |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.4 | ethambutol | Not assoc w R |
ethA | 4326632 | p.His281Pro | missense_variant | 0.63 | ethionamide | Uncertain significance |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.67 | ethionamide | |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 0.4 | 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 | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.41 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.32 | streptomycin | Not assoc w R |