Additional file 4: of ‘apparent’: a simple and flexible R package for accurate SNP-based parentage analysis in the absence of guiding information

Examples of the three different output files produced by the ‘apparent’ package. Worksheet 1: apparent-Triad-All, a complete sorted table of all 225,302 triads considered in the A. arguta example (only the first and last 10 rows are shown, to reduce file size). Worksheet 2: apparent-Triad-Sig, a reduced list reporting only those triads deemed true, based on the user-defined significance level (e.g. 99%). Worksheet 3: apparent-Dyad-Sig, the statistically significant results of the dyad analysis when the female parent of Family 1 (cv. ‘Dumbarton Oaks’) was removed from the population. (XLSX 51 kb)

‘apparent’软件包生成的三类不同输出文件示例。工作表1：apparent-Triad-All，即针对A. arguta示例中考量的全部225,302个三联体构建的完整排序表格（为缩减文件体积，仅展示前10行与后10行）。工作表2：apparent-Triad-Sig，即基于用户自定义显著性水平（如99%）筛选出的判定为真实的三联体精简列表。工作表3：apparent-Dyad-Sig，即移除种群中第1号家系（栽培品种‘Dumbarton Oaks’）的母本后开展双联体分析所得的具有统计学显著性的结果。（XLSX格式，51 kb）