Run ID: SRR28045372
Sample name:
Date: 2024-05-22T09:46:37.847044
Number of reads: 10889501
Percentage reads mapped: 99.48
Median coverage: 323.0
Strain: lineage4.2.2.2
Spoligotype:
Drug-resistance: Pre-XDR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2.2 | Euro-American (Ural) | None | 1.0 |
lineage4.2 | Euro-American | None | 1.0 |
lineage4 | Euro-American | None | 1.0 |
lineage4.2.2.2 | Euro-American (Ural) | None | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | rpoB | p.Gln432Pro | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | embB | p.Met306Val | Assoc w R | |
p.Gly406Ala | Assoc w R | |||
pyrazinamide | pncA | c.268_284delATCGAGGCGGTGTTCTA | Assoc w R | |
streptomycin | ||||
fluoroquinolones | ||||
moxifloxacin | gyrA | p.Asp94Asn | Assoc w R | High-level resistance |
ofloxacin | ||||
levofloxacin | gyrA | p.Asp94Asn | Assoc w R | |
ciprofloxacin | ||||
aminoglycosides | ||||
amikacin | ||||
capreomycin | ||||
kanamycin | ||||
cycloserine | ||||
ethionamide | ||||
clofazimine | ||||
para-aminosalicylic_acid | ||||
delamanid | ||||
bedaquiline | ||||
linezolid |
Gene | Chromosome position | Mutation | Type | Estimated fraction | Drugs | Confidence | Comment |
---|---|---|---|---|---|---|---|
gyrA | 7581 | p.Asp94Asn | missense_variant | 1.0 | levofloxacin | Assoc w R | |
moxifloxacin | Assoc w R | High-level resistance | |||||
rpoB | 761101 | p.Gln432Pro | missense_variant | 0.99 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288957 | c.268_284delATCGAGGCGGTGTTCTA | frameshift_variant | 0.32 | pyrazinamide | Assoc w R | |
embB | 4247429 | p.Met306Val | missense_variant | 0.62 | ethambutol | Assoc w R | |
embB | 4247730 | p.Gly406Ala | missense_variant | 0.42 | 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 | 8688 | p.Ala463Ser | 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 | 576077 | c.730C>T | synonymous_variant | 1.0 | ethionamide | Not assoc w R - Interim |
isoniazid | Not assoc w R | |||||
Rv0565c | 657425 | p.Gly16Ser | missense_variant | 1.0 | ethionamide | Uncertain significance |
rpoB | 762201 | p.Lys799Gln | missense_variant | 1.0 | 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 | 1.0 | linezolid | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrs | 1473295 | n.1450G>C | non_coding_transcript_exon_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
inhA | 1674414 | c.213G>A | synonymous_variant | 0.99 | ethionamide | Not assoc w R - Interim |
isoniazid | 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 |
bacA | 2063685 | c.1044G>A | synonymous_variant | 1.0 | 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 | 1.0 | streptomycin | Uncertain significance |
kanamycin | Uncertain significance | |||||
capreomycin | Not assoc w R | |||||
amikacin | 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 | |||||
Rv2681 | 2997680 | c.942A>C | synonymous_variant | 1.0 | capreomycin | |
Rv2752c | 3066280 | c.-89C>T | upstream_gene_variant | 1.0 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
thyX | 3068123 | c.-178A>C | upstream_gene_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 1.0 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | bedaquiline | Uncertain significance |
rifampicin | Not assoc w R | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
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 |