Table 1.

Single nucleotide polymorphism (SNP) accuracy, major allele accuracy, and minor allele accuracy of the remaining SNPs, after removing all SNPs with cross‐validation (CV) accuracy below the given threshold

CV‐accuracy threshold	Q‐05a	Q‐10a	Average	SD	Percentage of accurate SNPs (Number)	Percentage of SNPs left after filtering (Number)
No filter
Major allele accuracy	0.977	0.983	0.994	0.008	0.93 (2695603)
Minor allele accuracy	0.583	0.733	0.91	0.168
SNP accuracy	0.965	0.974	0.99	0.011
0.8
Major allele accuracy	0.97	0.981	0.994	0.008	0.9707 (2295485)	0.8204 (2364805)
Minor allele accuracy	0.8	0.852	0.954	0.08
SNP accuracy	0.96	0.974	0.992	0.01
0.85
Major allele accuracy	0.972	0.982	0.995	0.008	0.9775 (2118680)	0.752 (2167394)
Minor allele accuracy	0.826	0.875	0.962	0.069
SNP accuracy	0.965	0.974	0.992	0.01
0.9
Major allele accuracy	0.975	0.983	0.995	0.009	0.9876 (1818613)	0.6388 (1841310)
Minor allele accuracy	0.867	0.909	0.971	0.055
SNP accuracy	0.969	0.978	0.993	0.01
0.95
Major allele accuracy	0.98	0.986	0.996	0.008	0.999 (1230039)	0.4272 (1231243)
Minor allele accuracy	0.923	0.95	0.984	0.036
SNP accuracy	0.978	0.982	0.994	0.008

Values are given for one of the 20 test sets (for the other test sets, almost identical results were found). The average, standard deviation (SD) and quantiles were computed over all imputed SNPs with CV accuracy higher than the given threshold. Accurate SNPs are defined by a SNP accuracy (proportion of correctly imputed accessions) above 0.95.

^aQ‐5%, 5% quantile; Q‐10%, 10% quantile.