Run ID: ERR2041707
Sample name:
Date: 2024-03-26T13:23:32.631872
Number of reads: 1403003
Percentage reads mapped: 98.85
Median coverage: 39.0
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.His445Leu | Assoc w R | |
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ahpC | c.-48G>A | Uncertain significance | Mutation from literature | |
ethambutol | embB | p.Met306Ile | Assoc w R | |
pyrazinamide | pncA | p.Ala102Pro | 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 | 761140 | p.His445Leu | missense_variant | 1.0 | rifampicin | Assoc w R | |
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | isoniazid | Assoc w R | High-level resistance |
pncA | 2288938 | p.Ala102Pro | missense_variant | 1.0 | pyrazinamide | Assoc w R | |
ahpC | 2726145 | c.-48G>A | upstream_gene_variant | 1.0 | isoniazid | Uncertain significance | Mutation from literature |
embB | 4247431 | p.Met306Ile | 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 | 7547 | c.246C>T | synonymous_variant | 0.16 | levofloxacin | Not assoc w R - Interim |
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 | |||||
fgd1 | 491270 | p.Tyr163Cys | missense_variant | 1.0 | clofazimine | Uncertain significance |
pretomanid | ||||||
delamanid | 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 |
embR | 1417552 | c.-205G>A | upstream_gene_variant | 1.0 | ethambutol | |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | streptomycin | |
kanamycin | ||||||
capreomycin | ||||||
amikacin | ||||||
rrl | 1474571 | n.914G>A | non_coding_transcript_exon_variant | 1.0 | capreomycin | Uncertain significance |
linezolid | Uncertain significance | |||||
tsnR | 1854241 | c.636C>G | synonymous_variant | 1.0 | linezolid | 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 |
katG | 2154915 | c.1197A>G | synonymous_variant | 1.0 | isoniazid | Not assoc w R - Interim |
PPE35 | 2169041 | c.1572G>A | synonymous_variant | 0.35 | pyrazinamide | Not assoc w R - Interim |
PPE35 | 2169053 | c.1560T>C | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
PPE35 | 2169059 | c.1554G>A | synonymous_variant | 0.6 | pyrazinamide | |
PPE35 | 2169063 | p.Met517Thr | missense_variant | 1.0 | pyrazinamide | |
PPE35 | 2169065 | p.Ala516Ile | missense_variant | 0.6 | pyrazinamide | |
PPE35 | 2169068 | c.1545G>T | synonymous_variant | 0.6 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | clofazimine | Not assoc w R |
bedaquiline | Not assoc w R - Interim | |||||
Rv2752c | 3066501 | c.-310G>A | upstream_gene_variant | 1.0 | ethambutol | |
moxifloxacin | ||||||
levofloxacin | ||||||
rifampicin | ||||||
isoniazid | ||||||
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 | |||||
fbiA | 3640308 | c.-235C>T | upstream_gene_variant | 1.0 | clofazimine | |
pretomanid | ||||||
delamanid | ||||||
clpC1 | 4040471 | p.Ile78Met | missense_variant | 1.0 | pyrazinamide | Uncertain significance |
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 | 0.99 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
whiB6 | 4338785 | c.-264C>T | upstream_gene_variant | 1.0 | capreomycin | |
amikacin | ||||||
kanamycin | ||||||
gid | 4408084 | p.Glu40Gly | missense_variant | 1.0 | streptomycin | Uncertain significance |