Run ID: SRR12708376
Sample name:
Date: 2024-04-14T05:53:07.901431
Number of reads: 1318647
Percentage reads mapped: 99.41
Median coverage: 33.0
Strain: lineage2.2.1;lineage4.4.1.1
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.29 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.26 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.27 |
lineage4.4.1 | Euro-American (S-type) | None | 0.63 |
lineage4 | Euro-American | None | 0.76 |
lineage4.4.1.1 | Euro-American | None | 0.7 |
lineage4.4 | Euro-American | None | 0.69 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
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 | ||
ethambutol | ||||
pyrazinamide | pncA | c.-12T>C | Assoc w R | |
streptomycin | rrs | n.517C>T | 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 | 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 |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.26 | 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 | ||||||
rrs | 1472362 | n.517C>T | non_coding_transcript_exon_variant | 0.21 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.52 | 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 | |||||
inhA | 1674782 | p.Ile194Thr | missense_variant | 0.34 | isoniazid | Uncertain significance | Mutation from literature |
ethionamide | Uncertain significance | Mutation from literature | |||||
pncA | 2289253 | c.-12T>C | upstream_gene_variant | 0.23 | pyrazinamide | Assoc w R | |
ethR | 4327831 | p.Ala95Thr | missense_variant | 0.32 | ethionamide | Uncertain significance | Mutation from literature |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5462 | p.Val75Leu | missense_variant | 0.81 | 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 | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9138 | p.Gln613Glu | missense_variant | 0.83 | 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 | 0.34 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.35 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.23 | ethionamide | Not assoc w R - Interim |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.31 | rifampicin | Not assoc w R |
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 | 0.23 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 777416 | c.1065G>T | synonymous_variant | 0.65 | clofazimine | Not assoc w R - Interim |
bedaquiline | Not assoc w R - Interim | |||||
mmpS5 | 778979 | c.-74G>T | upstream_gene_variant | 0.36 | clofazimine | Uncertain significance |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.35 | 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 |
ndh | 2102990 | p.Val18Ala | missense_variant | 0.65 | ethionamide | Uncertain significance |
delamanid | Uncertain significance | |||||
isoniazid | Not assoc w R | |||||
katG | 2154724 | p.Arg463Leu | missense_variant | 0.32 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.2 | pyrazinamide | Not assoc w R |
PPE35 | 2168479 | p.Thr712Pro | missense_variant | 0.69 | pyrazinamide | Not assoc w R |
PPE35 | 2169840 | p.Gly258Asp | missense_variant | 0.77 | 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 | |||||
Rv2752c | 3065023 | p.Pro390Leu | missense_variant | 0.67 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3083 | 3448522 | p.Val7Phe | missense_variant | 0.75 | ethionamide | Uncertain significance |
Rv3083 | 3448608 | c.105G>A | synonymous_variant | 0.71 | ethionamide | Not assoc w R - Interim |
whiB7 | 3568779 | c.-100T>C | upstream_gene_variant | 0.48 | streptomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
Rv3236c | 3612665 | p.Val151Ala | missense_variant | 0.7 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.5 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
rpoA | 3877949 | p.Thr187Ala | missense_variant | 0.23 | rifampicin | Uncertain significance |
embC | 4238963 | c.-900C>T | upstream_gene_variant | 0.86 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.41 | ethambutol | Not assoc w R |
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 | 0.21 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.23 | streptomycin | Not assoc w R |