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JL Jinghui Li
ZW Zigui Wang
RF Rohan Fernando
HC Hao Cheng
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An Oryza sativa data set [15] with 413 Oryza sativa individual records of genotypes and the trait of flowering time in Arkansas was used to demonstrate the problem of spurious associations. After removing the records with missing data for the trait and genotypes with a minor allele frequency less than 0.05, 374 individuals and 33,701 SNPs were included in the analysis. The data are publicly available at the Rice Diversity Panel (http://www.ricediversity.org). Inferences of association based on genomic windows using Bayesian regression models were conducted using non-overlapping windows of size 1 Mb. The genome of the real data was divided into 378 non-overlapping genomic windows of size of 1 Mb, and the value of T was set to 1N, where N = 378. The lower, median and upper quartiles for the number of SNPs per window (pw) were 60, 82 and 106, respectively. Seven windows containing more than 175 (i.e., upper quartile + 1.5× (upper quartile − lower quartile)) SNPs were identified as dense.

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Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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