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. 2017 Oct 17;8:1792. doi: 10.3389/fpls.2017.01792

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Copyright © 2017 Bayer, Rapazote-Flores, Ganal, Hedley, Macaulay, Plieske, Ramsay, Russell, Shaw, Thomas and Waugh.

This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

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Boxplot of genotype call agreement rate (%) from the comparison of calls from the exome capture variant calling and the GenomeStudio calls for the accessions genotyped with the new 50k chip. The data shown is categorised by the provenance of the SNPs (9k = SNPs from the existing 9k chip, EXCAP SNPs = SNPs from exome capture data that are new and exclusive to the 50k chip), the source and type of cluster file (JH, James Hutton; TG, TraitGenetics, adjusted vs. unadjusted) and the source of the 50k genotype call set used (JH vs. TG). Bold horizontal lines represent the median, box boundaries upper and lower quartiles, whiskers maxima and minima, and open circles represent outliers.