Run ID: SRR25827529
Sample name:
Date: 2024-04-15T06:15:09.601736
Number of reads: 9202890
Percentage reads mapped: 99.22
Median coverage: 322.0
Strain: lineage2.2.1;lineage4.8
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.22 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.23 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.21 |
lineage4 | Euro-American | None | 0.78 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.79 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
p.Leu452Pro | 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 | embB | p.Met306Leu | Assoc w R | |
p.Gln497Arg | Assoc w R | |||
pyrazinamide | pncA | p.Gly132Ala | Assoc w R | |
p.Gln10Pro | 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 | eis | c.-10G>C | Uncertain significance | Mutation from literature |
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | thyX | c.-16C>T | Mutation from literature | |
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7570 | p.Ala90Val | missense_variant | 0.25 | 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) | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.16 | rifampicin | Assoc w R | |
rpoB | 761161 | p.Leu452Pro | missense_variant | 0.85 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 1.0 | streptomycin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 0.22 | 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 | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288847 | p.Gly132Ala | missense_variant | 0.2 | pyrazinamide | Assoc w R | |
pncA | 2289213 | p.Gln10Pro | missense_variant | 0.74 | pyrazinamide | Assoc w R | |
eis | 2715342 | c.-10G>C | upstream_gene_variant | 0.21 | kanamycin | Uncertain significance | Mutation from literature |
thyX | 3067961 | c.-16C>T | upstream_gene_variant | 0.22 | para-aminosalicylic_acid | Mutation from literature | |
embB | 4247429 | p.Met306Leu | missense_variant | 0.75 | ethambutol | Assoc w R | |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.23 | 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 | 0.24 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.23 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
fgd1 | 491290 | p.Val170Met | missense_variant | 0.25 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.19 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.17 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.21 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 656265 | c.1204_1205delAC | frameshift_variant | 0.78 | ethionamide | Uncertain significance |
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.24 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.21 | ethionamide | Uncertain significance |
nusG | 734658 | c.405A>G | synonymous_variant | 0.74 | rifampicin | Not assoc w R |
rpoB | 760315 | p.Val170Ala | missense_variant | 0.82 | rifampicin | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.25 | rifampicin | Not assoc w R |
rpoC | 764840 | p.Ile491Val | missense_variant | 0.18 | 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 | 0.22 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.22 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.18 | 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 | 0.22 | 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 | 0.18 | 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 | 0.85 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.22 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.25 | 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 | 0.2 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.18 | pyrazinamide | Not assoc w R |
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.88 | 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 | 0.76 | capreomycin | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.25 | cycloserine | |
whiB7 | 3568428 | c.252A>C | synonymous_variant | 0.13 | streptomycin | |
amikacin | ||||||
kanamycin | ||||||
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.23 | pyrazinamide | Not assoc w R - Interim |
Rv3236c | 3613636 | c.-520A>G | upstream_gene_variant | 0.8 | pyrazinamide | Not assoc w R |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.23 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.22 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
clpC1 | 4039729 | p.Asp326Asn | missense_variant | 0.77 | pyrazinamide | Not assoc w R |
embC | 4241022 | p.Ala387Val | missense_variant | 0.2 | ethambutol | Uncertain significance |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.19 | ethambutol | Not assoc w R |
embB | 4247015 | p.Ser168Ala | missense_variant | 0.13 | ethambutol | |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.23 | 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 | 0.24 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.23 | streptomycin | Not assoc w R |
gid | 4407620 | p.Tyr195His | missense_variant | 0.22 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.19 | streptomycin | Not assoc w R |