Table 1.

SNPs and filtering steps used for array design

Filter step	SNPs excluded	SNP count
None	0	24,528,374
Flanking sequence	18,619,172	5,909,202
Multi-allele SNP	7671	5,901,531
Confidencea	5,742,443	159,088
Illumina ADT score (<0.6)	33,556	125,532
Transversions	1318	124,214

^aSNP positions were filtered for high levels of heterozygous calls, biased allele ratio, or missing data as described in the Results section