Run ID: ERR4798816
Sample name:
Date: 2024-04-15T18:49:52.213623
Number of reads: 4303002
Percentage reads mapped: 99.65
Median coverage: 125.0
Strain: lineage2.2.1;lineage3;lineage4.1.1.3;lineage4.9
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.22 |
lineage2 | East-Asian | RD105 | 0.45 |
lineage4.1 | Euro-American | None | 0.09 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.46 |
lineage4.1.1.3 | Euro-American (X-type) | RD193 | 0.11 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.43 |
lineage4 | Euro-American | None | 0.34 |
lineage4.1.1 | Euro-American (X-type) | None | 0.11 |
lineage4.9 | Euro-American (H37Rv-like) | None | 0.2 |
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.Gly406Ser | Assoc w R | ||
pyrazinamide | pncA | c.391dupG | 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) |
p.Asp94Gly | Assoc w R | High-level resistance | ||
ofloxacin | ||||
levofloxacin | gyrA | p.Ala90Val | Assoc w R | |
p.Asp94Gly | Assoc w R | |||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | rrs | n.1401A>G | Assoc w R | |
capreomycin | rrs | n.1401A>G | Assoc w R | |
kanamycin | rrs | n.1401A>G | Assoc w R | |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.43 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.46 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.45 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.4 | streptomycin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.3 | capreomycin | Assoc w R | |
kanamycin | Assoc w R | ||||||
amikacin | Assoc w R | ||||||
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.44 | 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) |
ethionamide | Assoc w R | Alias fabG1_c.-15C>T | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.52 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288850 | c.391dupG | frameshift_variant | 0.46 | pyrazinamide | Assoc w R | |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.38 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247729 | p.Gly406Ser | missense_variant | 0.44 | 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 | 0.85 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.79 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.78 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.55 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.46 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.72 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.49 | ethionamide | Uncertain significance |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.24 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.19 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.65 | rifampicin | Not assoc w R |
rpoC | 764723 | p.Phe452Leu | missense_variant | 0.44 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.77 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.79 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.47 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.38 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 0.85 | streptomycin | Not assoc w R |
rplC | 800219 | c.-590T>C | upstream_gene_variant | 0.11 | linezolid | |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.62 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
fbiC | 1303326 | c.396C>T | synonymous_variant | 0.38 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.4 | 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 | 0.43 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.79 | 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 | 0.68 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.77 | pyrazinamide | Not assoc w R |
PPE35 | 2168686 | p.Thr643Ala | missense_variant | 0.12 | pyrazinamide | Uncertain significance |
Rv1979c | 2222357 | p.Thr270Ala | missense_variant | 0.48 | clofazimine | Uncertain significance |
bedaquiline | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 0.9 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2289047 | c.195C>T | synonymous_variant | 0.25 | pyrazinamide | Not assoc w R |
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.29 | pyrazinamide | |
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.22 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.19 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.85 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.47 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.85 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.44 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
alr | 3841473 | c.-53G>A | upstream_gene_variant | 0.26 | cycloserine | |
clpC1 | 4039799 | c.906C>T | synonymous_variant | 0.17 | pyrazinamide | |
panD | 4044858 | c.-577T>C | upstream_gene_variant | 0.2 | pyrazinamide | |
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.24 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.21 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embC | 4242075 | p.Arg738Gln | missense_variant | 0.23 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 0.81 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.11 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.35 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.48 | ethambutol | Not assoc w R |
whiB6 | 4338333 | c.188dupC | frameshift_variant | 0.45 | 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 | 0.85 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.66 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.47 | streptomycin | Not assoc w R |