Run ID: ERR3287597
Sample name:
Date: 2024-10-04T23:04:41.602259
Number of reads: 3780370
Percentage reads mapped: 99.8
Median coverage: 118.0
Strain: lineage4
Spoligotype:
Drug-resistance: MDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4 | Euro-American | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Asp435Tyr | Assoc w R | |
p.Asn437His | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB | ||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Gly406Ser | Assoc w R | |
pyrazinamide | pncA | c.284_286delACAinsC | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | ||||
ofloxacin | ||||
levofloxacin | ||||
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
rpoB | 761109 | p.Asp435Tyr | missense_variant | 1.0 | rifampicin | Assoc w R | |
rpoB | 761115 | p.Asn437His | missense_variant | 1.0 | rifampicin | Assoc w R - Interim | Expert rule: Non-silent variants in RRDR of rpoB |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288956 | c.284_286delACAinsC | frameshift_variant&missense_variant | 1.0 | pyrazinamide | Assoc w R | |
embB | 4247729 | p.Gly406Ser | missense_variant | 1.0 | ethambutol | 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 | 9304 | p.Gly668Asp | missense_variant | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
mshA | 575837 | c.490C>T | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
ethionamide | Not assoc w R - Interim | |||||
rpoB | 761889 | p.Val695Leu | missense_variant | 1.0 | rifampicin | Uncertain significance |
mmpL5 | 775639 | p.Ile948Val | missense_variant | 0.99 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
mmpL5 | 777875 | c.605delG | frameshift_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
mmpR5 | 779181 | c.198dupG | frameshift_variant | 1.0 | bedaquiline | Assoc w R |
clofazimine | Assoc w R | |||||
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rplC | 801009 | c.201A>G | synonymous_variant | 1.0 | linezolid | Not assoc w R - Interim |
fbiC | 1304918 | p.Thr663Asn | missense_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
rrs | 1471647 | n.-199G>A | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
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 |
ndh | 2101831 | c.1212G>A | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
delamanid | Not assoc w R - Interim | |||||
ethionamide | Not assoc w R - Interim | |||||
katG | 2156173 | c.-62C>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
Rv1979c | 2223214 | c.-50A>C | upstream_gene_variant | 1.0 | bedaquiline | Uncertain significance |
clofazimine | Uncertain significance | |||||
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
ahpC | 2726141 | c.-52C>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance |
Rv2752c | 3065517 | c.675C>T | synonymous_variant | 1.0 | levofloxacin | Not assoc w R - Interim |
moxifloxacin | Not assoc w R - Interim | |||||
isoniazid | Not assoc w R - Interim | |||||
rifampicin | Not assoc w R - Interim | |||||
ethambutol | Not assoc w R - Interim | |||||
thyA | 3074495 | c.-24C>T | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
Rv3236c | 3612219 | p.Val300Ile | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
rpoA | 3878635 | c.-128C>T | upstream_gene_variant | 0.26 | rifampicin | |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
ethA | 4328317 | c.-844C>T | upstream_gene_variant | 1.0 | ethionamide | |
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 | ||||||
gid | 4407967 | p.Leu79Trp | missense_variant | 1.0 | streptomycin | Uncertain significance |