Run ID: ERR4827458
Sample name:
Date: 2024-10-05T06:00:50.278898
Number of reads: 1156786
Percentage reads mapped: 99.43
Median coverage: 25.0
Strain: lineage4.3.3
Spoligotype:
Drug-resistance: HR-TB
Lineage | Family | RDs | Frequency |
---|---|---|---|
lineage4.3 | Euro-American (LAM) | None | 0.99 |
lineage4 | Euro-American | None | 1.0 |
lineage4.3.3 | Euro-American (LAM) | RD115 | 1.0 |
Drug | Resistance | Supporting mutations | WHO confidence | Comment |
---|---|---|---|---|
rifampicin | ||||
isoniazid | katG | p.Ser315Thr | Assoc w R | High-level resistance |
ethambutol | ||||
pyrazinamide | ||||
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 |
---|---|---|---|---|---|---|---|
katG | 2155168 | p.Ser315Thr | missense_variant | 1.0 | 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 | 1.0 | levofloxacin | Not assoc w R |
moxifloxacin | Not assoc w R | |||||
gyrA | 8040 | p.Gly247Ser | 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 | |||||
rpoC | 764995 | c.1626C>G | synonymous_variant | 1.0 | rifampicin | Not assoc w R |
rpoC | 766667 | p.Ser1100Ala | missense_variant | 1.0 | rifampicin | Uncertain significance |
rpsL | 781395 | c.-165T>C | upstream_gene_variant | 1.0 | streptomycin | Not assoc w R |
rrs | 1471659 | n.-187C>T | upstream_gene_variant | 1.0 | kanamycin | |
capreomycin | ||||||
streptomycin | ||||||
amikacin | ||||||
inhA | 1673346 | c.-856C>G | upstream_gene_variant | 0.16 | isoniazid | |
ethionamide | ||||||
inhA | 1673349 | c.-853G>C | upstream_gene_variant | 0.16 | isoniazid | |
ethionamide | ||||||
inhA | 1673380 | c.-822C>G | upstream_gene_variant | 0.35 | isoniazid | |
ethionamide | ||||||
tsnR | 1854300 | p.Leu232Pro | missense_variant | 1.0 | linezolid | Not assoc w R |
PPE35 | 2167865 | c.2748G>C | synonymous_variant | 0.16 | pyrazinamide | |
PPE35 | 2167868 | c.2745A>C | synonymous_variant | 0.17 | pyrazinamide | |
PPE35 | 2167965 | p.Ala883Gly | missense_variant | 0.15 | pyrazinamide | |
PPE35 | 2167967 | c.2646A>C | synonymous_variant | 0.15 | pyrazinamide | |
PPE35 | 2169293 | c.1320T>C | synonymous_variant | 0.12 | pyrazinamide | |
PPE35 | 2170048 | p.Leu189Val | missense_variant | 0.47 | pyrazinamide | |
PPE35 | 2170053 | p.Thr187Ser | missense_variant | 0.52 | pyrazinamide | |
Rv1979c | 2223293 | c.-129A>G | upstream_gene_variant | 1.0 | bedaquiline | Not assoc w R - Interim |
clofazimine | Not assoc w R | |||||
kasA | 2518919 | p.Gly269Ser | missense_variant | 1.0 | isoniazid | |
thyA | 3073868 | p.Thr202Ala | missense_variant | 1.0 | para-aminosalicylic_acid | |
ald | 3086788 | c.-32T>C | upstream_gene_variant | 1.0 | cycloserine | |
fbiD | 3339490 | p.Leu125Ile | missense_variant | 1.0 | pretomanid | |
delamanid | Uncertain significance | |||||
clofazimine | Uncertain significance | |||||
mtrB | 3625065 | p.Met517Leu | missense_variant | 1.0 | rifampicin | Not assoc w R |
bedaquiline | Uncertain significance | |||||
clpC1 | 4038287 | c.2418C>T | synonymous_variant | 1.0 | pyrazinamide | Not assoc w R |
embC | 4242643 | c.2781C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R |
embA | 4244823 | p.Val531Leu | missense_variant | 1.0 | ethambutol | Uncertain significance |
embB | 4248316 | c.1803C>T | synonymous_variant | 1.0 | ethambutol | Not assoc w R - Interim |
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 | 4408009 | p.Val65Ala | missense_variant | 1.0 | streptomycin | Uncertain significance |
gid | 4408156 | p.Leu16Arg | missense_variant | 1.0 | streptomycin | Not assoc w R |