High quality C-to-T SNPs from the genomes of 96 wild caught three-spine sticklebacks

To improve the methylation estimates in our study, we corrected for SNPs, which could have led to a wrong methylation call. The excluded positions were derived with custom written perl scripts from C-to-T and G-to-A-SNPs with genotype quality of 20 and a minimum allele frequency of 0.005 from the 96 wild caught three-spined sticklebacks with a combination of custom written Perl and R-scripts using packages from methylkit and GenomicRanges. This BED-file contains the C-to-T SNPs, in which the first field is the name of the chromosome; the second describes the start position and the third the end position of the feature in standard chromosomal coordinates.