Run ID: ERR10748563
Sample name:
Date: 2024-10-05T09:41:56.766835
Number of reads: 2811422
Percentage reads mapped: 99.26
Median coverage: 88.0
Strain: lineage2.2.1;lineage4.1.1.3;lineage4.3.2.1
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.17 |
lineage2 | East-Asian | RD105 | 0.54 |
lineage4.3.2 | Euro-American (LAM) | None | 0.18 |
lineage4.1 | Euro-American | None | 0.26 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.51 |
lineage4.1.1.3 | Euro-American (X-type) | RD193 | 0.26 |
lineage4.3.2.1 | Euro-American (LAM) | RD761 | 0.16 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.56 |
lineage4 | Euro-American | None | 0.47 |
lineage4.1.1 | Euro-American (X-type) | None | 0.26 |
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) |
p.Ile194Thr | Uncertain significance | Mutation from literature | ||
katG | p.Ser315Thr | Assoc w R | High-level resistance | |
ethambutol | embB | p.Met306Val | Assoc w R | |
pyrazinamide | pncA | p.Asp8Asn | Assoc w R | |
streptomycin | rrs | n.517C>T | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
p.Ile194Thr | Uncertain significance | Mutation from literature | ||
ethR | p.Ala95Thr | Uncertain significance | Mutation from literature | |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.72 | rifampicin | Assoc w R | |
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.5 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.44 | 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) | |||||
inhA | 1674782 | p.Ile194Thr | missense_variant | 0.5 | ethionamide | Uncertain significance | Mutation from literature |
isoniazid | Uncertain significance | Mutation from literature | |||||
katG | 2155168 | p.Ser315Thr | missense_variant | 0.42 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289220 | p.Asp8Asn | missense_variant | 0.46 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 0.6 | ethambutol | Assoc w R | |
ethR | 4327831 | p.Ala95Thr | missense_variant | 0.44 | ethionamide | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5520 | p.Pro94Leu | missense_variant | 0.16 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrB | 7222 | c.1983C>T | synonymous_variant | 0.28 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
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 | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.6 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.6 | isoniazid | Not assoc w R |
ethionamide | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.46 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.56 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.6 | ethionamide | Uncertain significance |
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.27 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.55 | rifampicin | Not assoc w R |
rpoC | 763555 | c.186C>T | synonymous_variant | 0.56 | rifampicin | Not assoc w R - Interim |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.14 | rifampicin | Not assoc w R |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.31 | rifampicin | Not assoc w R |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776100 | p.Thr794Ile | missense_variant | 0.46 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.55 | bedaquiline | Not assoc w R |
clofazimine | Not assoc w R | |||||
mmpS5 | 778979 | c.-74G>T | upstream_gene_variant | 0.61 | bedaquiline | Not assoc w R - Interim |
clofazimine | Uncertain significance | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.57 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rpsL | 781435 | c.-125G>C | upstream_gene_variant | 0.27 | streptomycin | Not assoc w R |
rplC | 800219 | c.-590T>C | upstream_gene_variant | 0.2 | linezolid | |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.61 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.53 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1472337 | n.492C>T | non_coding_transcript_exon_variant | 0.3 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | 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 | 0.99 | linezolid | Not assoc w R |
tlyA | 1917818 | c.-122C>T | upstream_gene_variant | 0.13 | capreomycin | |
tlyA | 1917972 | c.33A>G | synonymous_variant | 1.0 | capreomycin | Not assoc w R |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.54 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.65 | pyrazinamide | Not assoc w R |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
pncA | 2288856 | p.Asp129Ala | missense_variant | 0.17 | pyrazinamide | |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.17 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.63 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.56 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
rpoA | 3877956 | p.Glu184Asp | missense_variant | 0.23 | rifampicin | Uncertain significance |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.23 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.3 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.46 | ethambutol | Not assoc w R |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.24 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.55 | ethambutol | Not assoc w R |
whiB6 | 4338595 | c.-75delG | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.53 | streptomycin | Not assoc w R |
gid | 4407798 | c.405G>T | synonymous_variant | 0.22 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.6 | streptomycin | Not assoc w R |
gid | 4407973 | p.Val77Ala | missense_variant | 0.14 | streptomycin | Uncertain significance |
gid | 4408150 | p.Leu18Pro | missense_variant | 0.27 | streptomycin | |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.16 | streptomycin | Not assoc w R |