Table 2 Experiment 2 (296 maize lines), initial number of markers, number of filtered markers per chromosome, percentage of missing cells in the default imputation method, imputation method for short haplotypes, and imputation method for long haplotypes
ChromosomeInitial Number of Markers (% of Missing Cells Before Edit)Number of Edited Markers (% of Missing Cells After Filter)% Missing Cells After the Default Imputation% Missing Cells After Imputation Method for Short Haplotypes% Missing Cells After Imputation Method for Long Haplotypes
1108,292 (57.44)37,376 (51.66)48.7124.5833.65
282,006 (58.27)29,283 (52.23)49.3825.8733.95
377,207 (58.06)27,287 (51.85)48.7524.9333.95
466,512 (58.80)20,672 (51.87)49.2725.3233.96
577,067 (57.72)27,453 (51.80)48.7025.2733.14
655,489 (58.27)19,650 (51.92)48.7225.0333.71
757,504 (58.40)19,896 (52.33)49.5525.6632.99
858,568 (58.18)20,248 (51.80)48.0324.8732.67
950,473 (58.27)17,027 (51.95)49.2425.1433.40
1048,139 (58.84)16,373 (52.65)48.9524.4733.46
Total681,257235,265
  • 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.