Sequence quality determination and filtering of RADtags
The DNA from individual fish was digested with Eco RI and paired-end sequencing libraries with an insert size of 200–400 bp were constructed. These RAD libraries were subsequently sequenced using the Illumina HiSeq PE150 platform.
The raw sequence data were filtered by removal of reads with low-quality, reads with adapter contamination, reads with ≥ 10% unidentified nucleotides (N), and reads for which ≥ 50% of the length had a phred quality ≤ 5.