Run ID: ERR2707200
Sample name:
Date: 2024-10-04T14:38:31.897802
Number of reads: 4604143
Percentage reads mapped: 99.65
Median coverage: 145.0
Strain: lineage4.6.1.2
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.6 | Euro-American | None | 1.0 |
lineage4.6.1.2 | Euro-American | RD724 | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.6.1 | Euro-American (Uganda) | RD724 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Ser450Leu | Assoc w R | |
isoniazid | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | gid | c.398delC | Assoc w R | |
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | inhA | c.-777C>T | Assoc w R | Alias fabG1_c.-15C>T |
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761155 | p.Ser450Leu | missense_variant | 0.99 | rifampicin | Assoc w R | |
inhA | 1673425 | c.-777C>T | upstream_gene_variant | 1.0 | ethionamide | Assoc w R | Alias fabG1_c.-15C>T |
isoniazid | Assoc w R | Alias fabG1_c.-15C>T. Low-level resistance (multiple, genetically linked low-level resistance mutations are additive and confer high-level resistance) | |||||
gid | 4407804 | c.398delC | frameshift_variant | 1.0 | streptomycin | Assoc w R |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence |
---|---|---|---|---|---|---|
dnaA | 1302 | c.1302C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
gyrA | 7362 | p.Glu21Gln | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 7539 | p.Thr80Ala | missense_variant | 1.0 | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
hadA | 732110 | p.Cys61Gly | missense_variant | 1.0 | isoniazid | Uncertain significance |
rpoC | 764810 | p.Pro481Thr | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpoC | 764840 | p.Ile491Val | missense_variant | 1.0 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
embR | 1416410 | p.Leu313Arg | missense_variant | 1.0 | ethambutol | Uncertain significance |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
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 |
tlyA | 1917998 | p.Arg20Leu | missense_variant | 1.0 | capreomycin | Uncertain significance |
katG | 2154795 | p.Gln439His | missense_variant | 1.0 | isoniazid | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
eis | 2715271 | c.43_61dupGGGATGTTCCTACTGGCCG | frameshift_variant | 1.0 | kanamycin | Uncertain significance |
amikacin | Uncertain significance | |||||
ahpC | 2726141 | c.-52C>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
Rv2680 | 2996647 | c.543C>T | synonymous_variant | 1.0 | capreomycin | Not assoc w R - Interim |
Rv2681 | 2996876 | c.138A>C | synonymous_variant | 0.99 | capreomycin | Not assoc w R |
Rv2752c | 3065920 | p.Pro91Leu | missense_variant | 1.0 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
whiB7 | 3569029 | c.-350A>G | upstream_gene_variant | 1.0 | kanamycin | Not assoc w R |
amikacin | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
glpK | 4139670 | p.Cys29Tyr | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Uncertain significance | |||||
isoniazid | Uncertain significance | |||||
streptomycin | Uncertain significance | |||||
rifampicin | Uncertain significance | |||||
ethambutol | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4245055 | p.Thr608Asn | missense_variant | 1.0 | ethambutol | 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 | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin | ||||||
whiB6 | 4338787 | c.-266G>C | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
amikacin |