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. 2021 Sep 4;19(4):629–640. doi: 10.1016/j.gpb.2021.08.005

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© 2021 The Authors

This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).

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Fig. 5 — Interactive extraction of information for markers and individuals. GAPIT3 outputs two interactive HTML files to help user to extract information of markers on Manhattan plots (A) and QQ plots (B). The interactive plots are demonstrated on a trait simulated from the mouse genotypes with 12,564 SNPs on 1440 individuals (available at http://gscan.well.ox.ac.uk). The simulated trait had 75% heritability with 20 QTNs. When the cursor is moved over a dot, the marker information is displayed instantly, including name, P values, chromosome, position, and MAF. Similarly, a HTML file is generated to display the predicted phenotypes against observed phenotypes (C). When the cursor is moved over a dot, the individual information is displayed instantly, including name, as well as predicted and observed phenotypic values. When multiple prediction methods are used, individuals are displayed as different colors for different methods, such as gBLUP, cBLUP, and sBLUP.