Comparison of error rates for chromosome 10 SNPs from the AllZeaGBSv2.6 build for different levels of filtering by the Discovery SNP caller.

1Filters applied to the entire build (31,978 non-blank samples) 2Minimum sample size of 19 in at least one maize Nested Association Mapping (NAM) family 3Average error rates estimated from 5,254 NAM RILs. Median error rates were zero for all three filters. 4Average number of chromosome 10 SNPs with n > = 19 and MAF between 0.25 and 0.75 across the 25 NAM families. 5MAF > = 0.001, minimum FIT in inbred samples of 0.8, inbred coverage >0.15, inbred heterozygosity score <0.21.