User interface for results of Population Stratification analysis with the two-component PCA plot. The parameters used are shown in Additional file 2 : Table S3 (Run A). ① Four tabs in the main menu of the user interface with the ‘Population Stratification analysis’ tab selected; ② a radio button with a choice of three methods, namely PCA, Normalized PCs (each eigenvector is multiplied by the square root of its eigenvalue), and MDS; ③ two drop-down lists with values of principal components for which the PCA plot is drawn; ④ a drop-down list with the value ‘ALL’ or the ID/Name of the sample, which is displayed in a larger size compared to rest of the values; ⑤ a radio button with values ‘Hide’ and ‘Display’, which allows users to hide or show sample IDs/names; ⑥ the colors legend that matches groups/clusters with corresponding marker colors; ⑦ a button to download the results of the population stratification analysis as a ZIP file. The interactive two-component PCA plot displays the first and second principal components (PC1/PC2) for 141 accessions of rice varieties, with data point colors corresponding to 14 rice type groups. The symbol prime (') at the upper right of the numbers indicates selected items
