The frequency distribution of the position of each SNP in the RAD tag sequences discovered in the HX13-WL parents. After removal of the restriction site and barcode, and trimming the 3’end bases, 59 nucleotides remain. If putative SNPs were due to sequencing error, a significant enrichment of SNPs near the 3’ end of the RAD tag sequences would be expected. While a small peak in the 3’-end remains, the majority of bias has been removed and later data filtering not did not remove a larger percentage of SNPs from these locations.
Everett et al. BMC Genomics 2012 13:521 doi:10.1186/1471-2164-13-521