Table 1 Experiment 1 (504 doubled-haploid maize lines), initial number of markers per chromosome, number of filtered markers per chromosome, and percentage of missing cells per chromosome after imputation
ChromosomeInitial Number of Markers (% of Missing Cells Before Filter)Number of Markers After Filter (% of Missing Cells After Filter)% Missing Cells After Imputation
1108,292 (51.3)23,878 (43.37)19.67
282,006 (52.5)20,191 (44.63)20.95
377,207 (51.9)18,360 (44.02)20.52
466,512 (52.8)13,814 (44.58)20.48
577,067 (51.8)17,784 (43.78)19.78
655,489 (52.4)13,893 (44.23)20.84
757,504 (52.6)13,354 (44.52)20.82
858,568 (52.0)14,903 (43.99)20.67
950,473 (52.2)10,823 (43.30)19.53
1048,139 (52.7)11,281 (44.72)20.76
Total681,257158,281
  • Filter of markers consisted of deleting markers that had >80% of lines with missing values and deleting markers whose minor allele frequency was ≤0.05.