Run ID: ERR6358742
Sample name:
Date: 2024-04-15T00:08:30.205530
Number of reads: 7002996
Percentage reads mapped: 99.62
Median coverage: 212.0
Strain: lineage4.2.2.2;lineage4.6.1.2
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2.2 | Euro-American (Ural) | None | 0.3 |
lineage4.6 | Euro-American | None | 0.71 |
lineage4.2 | Euro-American | None | 0.31 |
lineage4.6.1.2 | Euro-American | RD724 | 0.69 |
lineage4 | Euro-American | None | 1.0 |
lineage4.6.1 | Euro-American (Uganda) | RD724 | 0.7 |
lineage4.2.2.2 | Euro-American (Ural) | None | 0.31 |
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 | pncA | p.His43Pro | Assoc w R - Interim | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ethA | c.1215_1224delGTTGAATTAC | 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 | 0.79 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.69 | isoniazid | Assoc w R | High-level resistance |
pncA | 2289114 | p.His43Pro | missense_variant | 0.69 | pyrazinamide | Assoc w R - Interim | |
embB | 4247429 | p.Met306Val | missense_variant | 0.7 | ethambutol | Assoc w R | |
ethA | 4326249 | c.1215_1224delGTTGAATTAC | frameshift_variant | 0.63 | 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 | 7539 | p.Thr80Ala | missense_variant | 0.66 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R - Interim | |||||
gyrA | 7585 | p.Ser95Thr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8688 | p.Ala463Ser | missense_variant | 0.32 | 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 | |||||
mshA | 576077 | c.730C>T | synonymous_variant | 0.31 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R | |||||
Rv0565c | 657425 | p.Gly16Ser | missense_variant | 0.36 | ethionamide | Uncertain significance |
rpoB | 761489 | c.1683G>A | synonymous_variant | 0.32 | rifampicin | Not assoc w R |
rpoC | 764660 | p.Val431Met | missense_variant | 0.68 | rifampicin | Uncertain significance |
rpoC | 764810 | p.Pro481Thr | missense_variant | 0.72 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 0.27 | linezolid | |
Rv1129c | 1254638 | c.-104C>T | upstream_gene_variant | 0.31 | moxifloxacin | |
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
embR | 1416410 | p.Leu313Arg | missense_variant | 0.7 | ethambutol | Uncertain significance |
embR | 1417485 | c.-138T>G | upstream_gene_variant | 0.3 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
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 |
bacA | 2063685 | c.1044G>A | synonymous_variant | 0.37 | streptomycin | Not assoc w R - Interim |
kanamycin | Not assoc w R - Interim | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
bacA | 2063911 | p.Ile273Thr | missense_variant | 0.33 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | Not assoc w R | |||||
PPE35 | 2170692 | c.-80T>G | upstream_gene_variant | 0.67 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
pncA | 2288800 | p.Arg148Cys | missense_variant | 0.3 | pyrazinamide | |
eis | 2714308 | p.Pro342Leu | missense_variant | 0.65 | amikacin | Uncertain significance |
kanamycin | Uncertain significance | |||||
Rv2681 | 2996876 | c.138A>C | synonymous_variant | 0.69 | capreomycin | Not assoc w R |
Rv2752c | 3065920 | p.Pro91Leu | missense_variant | 0.67 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
levofloxacin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 0.33 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.29 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.26 | cycloserine | |
whiB7 | 3569029 | c.-350A>G | upstream_gene_variant | 0.64 | streptomycin | Uncertain significance |
amikacin | Uncertain significance | |||||
kanamycin | Not assoc w R | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.27 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
glpK | 4139670 | p.Cys29Tyr | missense_variant | 0.72 | ethambutol | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
levofloxacin | Not assoc w R | |||||
rifampicin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245055 | p.Thr608Asn | missense_variant | 0.74 | ethambutol | Uncertain significance |
ubiA | 4269124 | p.Ala237Val | missense_variant | 0.69 | ethambutol | 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 | 4408094 | p.Gly37Arg | missense_variant | 0.68 | streptomycin | Uncertain significance |