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Raw data from the SNPDiscovery phase of the project is generated by sequencing the regions of interest (link to sequencing methods?). The Phred/Phrap/Polyphred suite of tools (link?) is then used to analyze the primary sequence traces. These sequences are ordered into a contig, and putative SNPs are identified.

Analysis of this data is useful for quality control, and can also be used exported into a format used by our primary genotyping system to select primers.