Run ID: SRR13232456
Sample name:
Date: 2024-04-16T00:57:57.906961
Number of reads: 4026405
Percentage reads mapped: 99.59
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 | 0.17 |
lineage2 | East-Asian | RD105 | 0.81 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.82 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.82 |
lineage4 | Euro-American | None | 0.18 |
lineage4.3.3 | Euro-American (LAM) | RD115 | 0.19 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Val | Assoc w R | |
p.Gly406Ala | Assoc w R | |||
pyrazinamide | pncA | p.Ile31Ser | Assoc w R | |
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
rrs | n.514A>C | Assoc w R | ||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
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 | ethA | c.341delA | Assoc w R | |
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 | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.76 | streptomycin | Assoc w R | |
rrs | 1472359 | n.514A>C | non_coding_transcript_exon_variant | 0.32 | streptomycin | Assoc w R | |
rrs | 1473246 | n.1401A>G | non_coding_transcript_exon_variant | 0.73 | kanamycin | Assoc w R | |
capreomycin | Assoc w R | ||||||
amikacin | Assoc w R | ||||||
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289150 | p.Ile31Ser | missense_variant | 0.8 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 0.18 | ethambutol | Assoc w R | |
embB | 4247730 | p.Gly406Ala | missense_variant | 0.8 | ethambutol | Assoc w R | |
ethA | 4327132 | c.341delA | frameshift_variant | 0.8 | ethionamide | 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 | 8040 | p.Gly247Ser | missense_variant | 0.19 | 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 | |||||
Rv0010c | 13287 | p.Glu91Gly | missense_variant | 0.8 | isoniazid | |
Rv0010c | 13471 | p.Leu30Val | missense_variant | 0.18 | isoniazid | Uncertain significance |
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.77 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.85 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
mshA | 576108 | p.Ala254Gly | missense_variant | 0.2 | ethionamide | |
isoniazid | ||||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.85 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.8 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.81 | ethionamide | Uncertain significance |
hadA | 731688 | c.-242C>T | upstream_gene_variant | 0.23 | isoniazid | |
rpoB | 762477 | p.Lys891Glu | missense_variant | 0.81 | rifampicin | Uncertain significance |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.83 | rifampicin | Not assoc w R |
rpoC | 764817 | p.Val483Ala | missense_variant | 0.2 | rifampicin | Uncertain significance |
rpoC | 764995 | c.1626C>G | synonymous_variant | 0.2 | 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 | 0.79 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.76 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.79 | 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 | 0.85 | moxifloxacin | Not assoc w R |
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
fbiC | 1303095 | c.165G>A | synonymous_variant | 0.15 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
sigE | 1365139 | p.His243Tyr | missense_variant | 0.16 | pyrazinamide | |
Rv1258c | 1406760 | c.580_581insC | frameshift_variant | 0.79 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
inhA | 1674305 | p.Gln35Arg | missense_variant | 0.22 | ethionamide | Uncertain significance |
isoniazid | Uncertain significance | |||||
rpsA | 1834022 | p.Leu161Met | missense_variant | 0.14 | pyrazinamide | Uncertain significance |
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.83 | pyrazinamide | Not assoc w R - Interim |
rpsA | 1834836 | p.Met432Thr | missense_variant | 0.18 | 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 |
katG | 2154724 | p.Arg463Leu | missense_variant | 0.78 | isoniazid | Not assoc w R |
katG | 2156196 | c.-85C>T | upstream_gene_variant | 0.24 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.86 | 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 | |||||
kasA | 2518919 | p.Gly269Ser | missense_variant | 0.14 | isoniazid | |
folC | 2746340 | p.Ala420Val | missense_variant | 0.18 | para-aminosalicylic_acid | |
ribD | 2986827 | c.-12G>A | upstream_gene_variant | 0.81 | para-aminosalicylic_acid | |
thyA | 3073868 | p.Thr202Ala | missense_variant | 0.23 | para-aminosalicylic_acid | |
ald | 3086731 | c.-89A>G | upstream_gene_variant | 0.84 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.85 | pyrazinamide | Not assoc w R - Interim |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.78 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 0.15 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4243346 | c.114A>G | synonymous_variant | 0.85 | ethambutol | Not assoc w R - Interim |
embA | 4243460 | c.228C>T | synonymous_variant | 0.83 | ethambutol | Not assoc w R |
embA | 4244138 | c.906G>A | synonymous_variant | 0.86 | ethambutol | Not assoc w R - Interim |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.82 | ethambutol | Not assoc w R |
ethA | 4326299 | p.Thr392Arg | missense_variant | 0.29 | ethionamide | Uncertain significance |
whiB6 | 4338371 | p.Thr51Pro | missense_variant | 0.73 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
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 | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4407588 | c.615A>G | synonymous_variant | 0.89 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.85 | streptomycin | Not assoc w R |
gid | 4408156 | p.Leu16Arg | missense_variant | 0.21 | streptomycin | Not assoc w R |