Run ID: SRR18715461
Sample name:
Date: 2024-10-05T07:42:47.972302
Number of reads: 3925307
Percentage reads mapped: 99.54
Median coverage: 113.0
Strain: lineage2.2.1;lineage4.3.3
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.1 |
lineage2 | East-Asian | RD105 | 0.89 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.88 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.87 |
lineage4 | Euro-American | None | 0.13 |
lineage4.3.3 | Euro-American (LAM) | RD115 | 0.11 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
rpoC | p.Gly332Arg | Uncertain significance | Mutation from literature | |
p.Asp485Asn | Uncertain significance | Mutation from literature | ||
isoniazid | katG | p.Ile335Val | Uncertain significance | Mutation from literature |
p.Ser315Thr | Assoc w R | High-level resistance | ||
ethambutol | embB | p.Gly406Asp | Assoc w R | |
p.Gln497Arg | Assoc w R | |||
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpoC | 764363 | p.Gly332Arg | missense_variant | 0.69 | rifampicin | Uncertain significance | Mutation from literature |
rpoC | 764822 | p.Asp485Asn | missense_variant | 0.93 | rifampicin | Uncertain significance | Mutation from literature |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.86 | streptomycin | Assoc w R | |
katG | 2155109 | p.Ile335Val | missense_variant | 0.85 | isoniazid | Uncertain significance | Mutation from literature |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
embB | 4247730 | p.Gly406Asp | missense_variant | 0.12 | ethambutol | Assoc w R | |
embB | 4248003 | p.Gln497Arg | missense_variant | 0.89 | 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 | 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 | 0.86 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.94 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.91 | ethionamide | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.89 | rifampicin | Not assoc w R |
rpoC | 763612 | p.Glu81Asp | missense_variant | 0.69 | rifampicin | |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.13 | rifampicin | Not assoc w R |
rpoC | 766488 | p.Pro1040Arg | missense_variant | 0.14 | rifampicin | Uncertain significance |
rpoC | 766667 | p.Ser1100Ala | missense_variant | 0.12 | rifampicin | Uncertain significance |
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 | 0.88 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.85 | bedaquiline | |
clofazimine | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.87 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
fbiC | 1302917 | c.-14_-13insA | upstream_gene_variant | 0.83 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.95 | streptomycin | Uncertain significance |
pyrazinamide | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.88 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834776 | p.Ala412Val | missense_variant | 0.9 | pyrazinamide | Uncertain significance |
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 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.91 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.81 | 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 | |||||
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.13 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
fbiD | 3339490 | p.Leu125Ile | missense_variant | 0.13 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.91 | 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 | 0.88 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
fbiA | 3640879 | c.337C>T | synonymous_variant | 0.85 | pretomanid | |
delamanid | Not assoc w R - Interim | |||||
clofazimine | Not assoc w R - Interim | |||||
alr | 3840953 | c.468C>T | synonymous_variant | 0.16 | cycloserine | |
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.16 | pyrazinamide | 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 | 0.82 | ethambutol | Not assoc w R |
embA | 4243598 | c.366G>A | synonymous_variant | 0.87 | ethambutol | Not assoc w R - Interim |
embA | 4244823 | p.Val531Leu | missense_variant | 0.14 | ethambutol | Uncertain significance |
embB | 4247872 | c.1359C>T | synonymous_variant | 0.87 | ethambutol | Not assoc w R - Interim |
embB | 4248316 | c.1803C>T | synonymous_variant | 0.22 | ethambutol | Not assoc w R - Interim |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.88 | ethambutol | Not assoc w R |
ethA | 4326474 | p.Pro334Ala | missense_variant | 0.88 | ethionamide | Uncertain significance |
whiB6 | 4338326 | p.Ala66Thr | missense_variant | 0.87 | kanamycin | Uncertain significance |
capreomycin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
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 | 0.99 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.9 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.87 | streptomycin | Not assoc w R |
gid | 4408009 | p.Val65Ala | missense_variant | 0.13 | streptomycin | Uncertain significance |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.14 | streptomycin | Not assoc w R |