Table 2.

Summary of SNP numbers during the selection process.

SNP set description	# SNPs
Total number called in 170 sample set	20,560,627
After filtering	528,439
Submitted to Illumina ADT (chr 1H-7H only)	519,742
Passed ADT analysis	295,642
Max. gene coverage set	16,957
Max. chromo coverage + gene evenness set	26,091
Total number from exome capture pre redundancy check	43,048
Overlap between 9k and EXCAP set	732
Legacy markers in design carried forward from 9k chip	6,951
Exome capture markers in design post redundancy check	42,316
Final number for array design	49,267
Total number of working assays on 50k chip	44,040 (6,251 from 9k + 37,789 from EXCAP)
Total number of scorable assays on 50k chip	43,461