Run ID: ERR108464
Sample name:
Date: 2024-10-03T23:36:45.295632
Number of reads: 4624684
Percentage reads mapped: 99.44
Median coverage: 98.0
Strain: lineage4.2.1;lineage4.8
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.2 | Euro-American | None | 0.83 |
lineage4 | Euro-American | None | 1.0 |
lineage4.8 | Euro-American (mainly T) | RD219 | 0.19 |
lineage4.2.1 | Euro-American (TUR) | None | 0.84 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | ||||
streptomycin | rpsL | p.Lys43Arg | Assoc w R | |
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 |
---|---|---|---|---|---|---|---|
rpsL | 781687 | p.Lys43Arg | missense_variant | 0.86 | streptomycin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 0.89 | isoniazid | Assoc w R | High-level resistance |
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 | 0.89 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 9304 | p.Gly668Asp | missense_variant | 0.9 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
Rv0010c | 13441 | p.Thr40Pro | missense_variant | 0.16 | isoniazid | Uncertain significance |
Rv0010c | 13454 | c.105C>T | synonymous_variant | 0.14 | isoniazid | Not assoc w R - Interim |
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 |
rplC | 800204 | c.-605T>C | upstream_gene_variant | 0.8 | linezolid | |
Rv1129c | 1254582 | c.-48A>G | upstream_gene_variant | 0.18 | levofloxacin | Uncertain significance |
moxifloxacin | Uncertain significance | |||||
isoniazid | Not assoc w R | |||||
rifampicin | Not assoc w R | |||||
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
rrl | 1474001 | n.344C>T | non_coding_transcript_exon_variant | 0.12 | capreomycin | Not assoc w R |
linezolid | Not assoc w R | |||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 0.8 | 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 | 0.83 | kanamycin | Not assoc w R - Interim |
capreomycin | Not assoc w R | |||||
streptomycin | Not assoc w R - Interim | |||||
amikacin | Not assoc w R | |||||
bacA | 2063911 | p.Ile273Thr | missense_variant | 0.84 | kanamycin | Uncertain significance |
capreomycin | Not assoc w R | |||||
streptomycin | Uncertain significance | |||||
amikacin | Not assoc w R | |||||
PPE35 | 2168149 | p.Pro822Ser | missense_variant | 0.19 | pyrazinamide | Not assoc w R |
PPE35 | 2169879 | p.Phe245Cys | missense_variant | 0.89 | pyrazinamide | Uncertain significance |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
Rv2680 | 2995848 | c.-257G>A | upstream_gene_variant | 0.12 | capreomycin | |
ald | 3086742 | c.-78A>C | upstream_gene_variant | 0.9 | cycloserine | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 0.89 | cycloserine | |
mtrB | 3625065 | p.Met517Leu | missense_variant | 0.92 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
mtrB | 3625403 | p.Val404Ala | missense_variant | 0.85 | rifampicin | Uncertain significance |
bedaquiline | Uncertain significance | |||||
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embB | 4249354 | c.2841G>C | synonymous_variant | 0.21 | ethambutol | Not assoc w R - Interim |
embB | 4249594 | c.3081G>A | synonymous_variant | 0.79 | ethambutol | Not assoc w R - Interim |
ethR | 4327937 | p.Thr130Ile | missense_variant | 0.16 | ethionamide | |
ethA | 4328376 | c.-903G>C | upstream_gene_variant | 0.87 | 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 | 4338598 | c.-77G>C | upstream_gene_variant | 0.11 | kanamycin | |
capreomycin | ||||||
amikacin | Uncertain significance | |||||
whiB6 | 4338732 | c.-211C>T | upstream_gene_variant | 0.92 | kanamycin | |
capreomycin | ||||||
amikacin |