Run ID: SRR25827717
Sample name:
Date: 2024-03-26T13:14:45.376906
Number of reads: 9232791
Percentage reads mapped: 98.79
Median coverage: 307.0
Strain: lineage2.2.1.1;lineage3;lineage4
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage3 | East-African-Indian | RD750 | 0.23 |
lineage2 | East-Asian | RD105 | 0.67 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.65 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.66 |
lineage4 | Euro-American | None | 0.1 |
lineage2.2.1.1 | East-Asian (Beijing) | RD105;RD207;RD181;RD150 | 0.17 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Cys | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
rpoC | p.Ile491Thr | Uncertain significance | Mutation from literature | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embA | c.-16C>T | Uncertain significance | Mutation from literature |
embB | p.Met306Val | Assoc w R | ||
pyrazinamide | pncA | p.Asp49Glu | Assoc w R - Interim | |
p.Ile5Ser | Assoc w R | |||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Gly | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Gly | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | thyA | p.Thr22Ala | Mutation from literature | |
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.55 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761155 | p.Ser450Cys | missense_variant | 0.22 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
rpoC | 764841 | p.Ile491Thr | missense_variant | 0.16 | rifampicin | Uncertain significance | Mutation from literature |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.56 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289095 | p.Asp49Glu | missense_variant | 0.14 | pyrazinamide | Assoc w R - Interim | |
pncA | 2289228 | p.Ile5Ser | missense_variant | 0.13 | pyrazinamide | Assoc w R | |
thyA | 3074408 | p.Thr22Ala | missense_variant | 0.15 | para-aminosalicylic_acid | Mutation from literature | |
embA | 4243217 | c.-16C>T | upstream_gene_variant | 0.22 | ethambutol | Uncertain significance | Mutation from literature |
embB | 4247429 | p.Met306Val | missense_variant | 0.45 | ethambutol | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 6963 | p.Arg575His | missense_variant | 0.25 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
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 | 491290 | p.Val170Met | missense_variant | 0.23 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
fgd1 | 491742 | c.960T>C | synonymous_variant | 0.9 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.72 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620553 | c.663T>C | synonymous_variant | 0.31 | capreomycin | Not assoc w R |
amikacin | Not assoc w R - Interim | |||||
kanamycin | Not assoc w R - Interim | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.62 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.89 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.63 | ethionamide | Uncertain significance |
rpoB | 759746 | c.-61C>T | upstream_gene_variant | 0.26 | rifampicin | Not assoc w R |
rpoB | 762434 | c.2628T>G | synonymous_variant | 0.24 | rifampicin | Not assoc w R |
rpoB | 763031 | c.3225T>C | synonymous_variant | 0.87 | rifampicin | Not assoc w R |
rpoC | 764363 | p.Gly332Ser | missense_variant | 0.16 | rifampicin | Uncertain significance |
rpoC | 764817 | p.Val483Ala | missense_variant | 0.37 | 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 | 0.91 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776181 | p.Asp767Thr | missense_variant | 0.17 | clofazimine | |
bedaquiline | ||||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.64 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
Rv1129c | 1253956 | p.Gln193His | missense_variant | 0.21 | moxifloxacin | |
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.91 | 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 | 0.61 | streptomycin | Uncertain significance |
isoniazid | Uncertain significance | |||||
pyrazinamide | Uncertain significance | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rpsA | 1834177 | c.636A>C | synonymous_variant | 0.64 | pyrazinamide | Not assoc w R - Interim |
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.99 | 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 | 0.92 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.92 | 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 | |||||
pncA | 2289365 | c.-125delC | upstream_gene_variant | 0.24 | pyrazinamide | |
eis | 2714846 | p.Val163Ile | missense_variant | 0.15 | amikacin | Not assoc w R |
kanamycin | Not assoc w R | |||||
ahpC | 2726105 | c.-88G>A | upstream_gene_variant | 0.19 | isoniazid | Not assoc w R |
Rv2477c | 2782498 | c.1545C>T | synonymous_variant | 0.23 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
kanamycin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
thyX | 3067949 | c.-4C>T | upstream_gene_variant | 0.27 | 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 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
mtrB | 3626562 | p.Pro18Ser | missense_variant | 0.65 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3640211 | c.-332T>G | upstream_gene_variant | 0.4 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
alr | 3841578 | c.-158G>A | upstream_gene_variant | 0.25 | cycloserine | |
alr | 3841590 | c.-170G>A | upstream_gene_variant | 0.25 | cycloserine | |
panD | 4044872 | c.-591C>T | upstream_gene_variant | 0.2 | pyrazinamide | |
glpK | 4138622 | c.1134C>T | synonymous_variant | 0.2 | ethambutol | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
isoniazid | Not assoc w R | |||||
embC | 4240827 | p.Ala322Gly | missense_variant | 0.22 | ethambutol | |
embC | 4241022 | p.Ala387Val | missense_variant | 0.2 | ethambutol | Uncertain significance |
embC | 4242075 | p.Arg738Gln | missense_variant | 0.22 | 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 | 0.68 | ethambutol | Not assoc w R |
embA | 4245303 | c.2071C>T | synonymous_variant | 0.24 | ethambutol | Not assoc w R - Interim |
embA | 4245835 | p.Leu868Arg | missense_variant | 0.21 | ethambutol | |
embB | 4247015 | p.Ser168Ala | missense_variant | 0.21 | ethambutol | |
embB | 4247847 | p.Gln445Arg | missense_variant | 0.18 | ethambutol | Uncertain significance |
embB | 4248115 | c.1602C>T | synonymous_variant | 0.19 | ethambutol | Not assoc w R |
embB | 4249757 | p.Thr1082Ala | missense_variant | 0.31 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.61 | ethambutol | Not assoc w R |
aftB | 4268719 | p.Asn40Asp | missense_variant | 0.21 | ethambutol | Uncertain significance |
whiB6 | 4338292 | p.Ala77Val | missense_variant | 0.17 | capreomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
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 | 0.86 | streptomycin | Not assoc w R |
gid | 4407620 | p.Tyr195His | missense_variant | 0.17 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.62 | streptomycin | Not assoc w R |
gid | 4408070 | p.Trp45Arg | missense_variant | 0.22 | streptomycin | Uncertain significance |