Table 2.

SNP calls remaining after sequential filtration of downsampling experiment data

Sequential filtration	Exp1	Exp2
None	5090	1616
After F1a	4500	1449
After F2b	4055 (2304)c	1343 (545)c
After MD filter >20%d	550 (347)c	320 (132)c
After MD filter >10%d	113 (61)c	63 (20)c
After MD filter ≥5%d	20 (6)c	10 (3)c

^aRemoval of markers with >1 SNP in the same sequence

^bRemoval of markers in which the SNP occurs in the first 9 bases of sequence

^cSubset of markers meeting criterion of chi-square value ≤ 20

^dRemoval of markers in which >20%, >10% or ≥5% of 217 individuals have missing data, as indicated