Table 4 Statistics describing the distribution of different properties of RAD sequences after each step of filtering (FASTX-Toolkit), alignment to the eel draft genome (BOWTIE) and assemblage into loci (STACKS) in silver eels (SE) and glass eels (GE)
From: Signatures of natural selection between life cycle stages separated by metamorphosis in European eel
FASTX | |||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|
Group | Raw reads | Filtered reads | % Eliminated | Mean Q | Q1 | Med | Q3 | % A | % C | % G | % T |
SE | 12234656 | 10692256 | 13.2 | 38.7 | 38 | 39.7 | 40 | 28.7 | 22.0 | 20.4 | 28.7 |
GE | 9593701 | 7899505 | 17.8 | 38.7 | 38 | 39.4 | 40.2 | 29.5 | 20.7 | 20.4 | 29.4 |
BOWTIE | |||||||||||
Group | Reads | Aligned | % Aligned | Non-aligned | % Non-aligned | Discarded | % Discarded | ||||
SE | 10692256 | 7433827 | 69.3 | 2782716 | 26.3 | 475668 | 4.5 | ||||
GE | 7899505 | 5527660 | 70.0 | 2018833 | 26.0 | 353043 | 4.5 | ||||
STACKS | |||||||||||
Group | Reads | Stacks | Loci | Loci used | % Loci used | Loci discarded | % Loci discarded | ||||
SE | 7433827 | 547017 | 348342 | 253864 | 73.9 | 94482 | 27.1 | ||||
GE | 5527660 | 526821 | 335343 | 217326 | 64.5 | 118016 | 35.5 | ||||