Run ID: ERR4797417
Sample name:
Date: 2024-04-15T16:20:49.692496
Number of reads: 3735416
Percentage reads mapped: 99.55
Median coverage: 110.0
Strain: lineage2.2.1.1;lineage4.1.1.1
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage2 | East-Asian | RD105 | 0.28 |
lineage4.1 | Euro-American | None | 0.75 |
lineage4.1.1.1 | Euro-American (X-type) | RD183 | 0.7 |
lineage2.2.1 | East-Asian (Beijing) | RD105;RD207;RD181 | 0.26 |
lineage2.2 | East-Asian (Beijing) | RD105;RD207 | 0.22 |
lineage4 | Euro-American | None | 0.73 |
lineage4.1.1 | Euro-American (X-type) | None | 0.76 |
lineage2.2.1.1 | East-Asian (Beijing) | RD105;RD207;RD181;RD150 | 0.23 |
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 | |
pyrazinamide | ||||
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 | ethA | c.1242delT | Assoc w R | |
c.754_755dupGC | Assoc w R | |||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7582 | p.Asp94Gly | missense_variant | 0.22 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.23 | rifampicin | Assoc w R | |
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.27 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.34 | isoniazid | Assoc w R | High-level resistance |
embB | 4247429 | p.Met306Val | missense_variant | 0.37 | ethambutol | Assoc w R | |
ethA | 4326231 | c.1242delT | frameshift_variant | 0.2 | ethionamide | Assoc w R | |
ethA | 4326718 | c.754_755dupGC | frameshift_variant | 0.12 | ethionamide | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
gyrB | 5936 | p.Ala233Pro | missense_variant | 0.1 | 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 | 491742 | c.960T>C | synonymous_variant | 0.23 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
mshA | 575907 | p.Ala187Val | missense_variant | 0.24 | ethionamide | Not assoc w R |
isoniazid | Not assoc w R | |||||
ccsA | 620625 | p.Ile245Met | missense_variant | 0.22 | capreomycin | Not assoc w R |
amikacin | Not assoc w R | |||||
kanamycin | Uncertain significance | |||||
Rv0565c | 657081 | c.390G>A | synonymous_variant | 0.31 | ethionamide | Not assoc w R - Interim |
Rv0565c | 657142 | p.Arg110His | missense_variant | 0.33 | ethionamide | Uncertain significance |
Rv0565c | 657269 | p.Ser68Pro | missense_variant | 0.51 | ethionamide | Uncertain significance |
rpoB | 761292 | p.Val496Met | missense_variant | 0.13 | rifampicin | Uncertain significance |
rpoC | 764363 | p.Gly332Ser | missense_variant | 0.13 | rifampicin | Uncertain significance |
rpoC | 765150 | p.Gly594Glu | missense_variant | 0.78 | 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 | 0.25 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
mmpL5 | 776182 | p.Asp767Asn | missense_variant | 0.25 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R | |||||
mmpS5 | 779615 | c.-710C>G | upstream_gene_variant | 0.27 | clofazimine | |
bedaquiline | ||||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800219 | c.-590T>C | upstream_gene_variant | 0.76 | linezolid | |
Rv1129c | 1254562 | c.-28T>C | upstream_gene_variant | 0.26 | 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 | 0.24 | 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 | 0.27 | 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 | 0.28 | isoniazid | Not assoc w R |
PPE35 | 2167926 | p.Leu896Ser | missense_variant | 0.25 | pyrazinamide | Not assoc w R |
PPE35 | 2167967 | c.2645dupC | frameshift_variant | 0.76 | pyrazinamide | Uncertain significance |
PPE35 | 2168034 | p.Thr860Ile | missense_variant | 0.74 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
eis | 2714846 | p.Val163Ile | missense_variant | 0.24 | amikacin | Not assoc w R |
kanamycin | Not assoc w R | |||||
Rv2477c | 2782877 | p.Val389Ala | missense_variant | 0.69 | ethambutol | |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
kanamycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
amikacin | Uncertain significance | |||||
thyA | 3074282 | p.Arg64Cys | missense_variant | 0.18 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.9 | cycloserine | |
ald | 3087711 | p.Val298Met | missense_variant | 0.17 | cycloserine | |
Rv3236c | 3612813 | p.Thr102Ala | missense_variant | 0.22 | 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 | 0.19 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
fbiA | 3641238 | c.696G>A | synonymous_variant | 0.66 | clofazimine | Not assoc w R - Interim |
pretomanid | ||||||
delamanid | Not assoc w R - Interim | |||||
fbiA | 3641447 | p.Thr302Met | missense_variant | 0.77 | clofazimine | Not assoc w R |
pretomanid | ||||||
delamanid | Uncertain significance | |||||
rpoA | 3877553 | p.Glu319Lys | missense_variant | 0.67 | rifampicin | Not assoc w R |
embC | 4239656 | c.-207C>T | upstream_gene_variant | 0.77 | ethambutol | Uncertain significance |
embC | 4240897 | c.1035C>G | synonymous_variant | 0.79 | ethambutol | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embC | 4242803 | p.Val981Leu | missense_variant | 0.68 | ethambutol | Not assoc w R |
embA | 4243460 | c.228C>T | synonymous_variant | 0.17 | ethambutol | Not assoc w R |
embB | 4246746 | p.Asp78Gly | missense_variant | 0.74 | ethambutol | Uncertain significance |
embB | 4247880 | p.Val456Ala | missense_variant | 0.29 | ethambutol | Uncertain significance |
embB | 4248115 | c.1602C>T | synonymous_variant | 0.4 | ethambutol | Not assoc w R |
embB | 4249408 | c.2895G>A | synonymous_variant | 0.76 | ethambutol | Not assoc w R |
aftB | 4267647 | p.Asp397Gly | missense_variant | 0.14 | ethambutol | Not assoc w R |
ubiA | 4269245 | p.His197Tyr | missense_variant | 0.73 | ethambutol | |
whiB6 | 4338410 | p.Pro38Ala | missense_variant | 0.16 | 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 | 0.17 | streptomycin | Not assoc w R |
gid | 4407927 | p.Glu92Asp | missense_variant | 0.26 | streptomycin | Not assoc w R |
gid | 4408266 | c.-64C>G | upstream_gene_variant | 0.1 | streptomycin |