Basic SNP characteristics using different filter settings for missing data. Basic SNP characteristics using different filter settings for missing data.

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Basic SNP characteristics using different filter settings for missing data. Basic SNP characteristics using different filter settings for missing data. Shown are histograms representing the number of SNP sites that exhibit a certain sample coverage (A), minor allele frequency (B, C, E, and G), or proportion of heterozygous sites (D, F, and H). Data are from 813 F2 plants from the fall 2014 population, and were generated using the TASSEL 4 site report function. For (A) and (B), unfiltered data directly after SNP calling was used. For (C)–(H), SNP sites were filtered by the indicated proportion of missing data per sample, but no further data imputation or error correction was performed. Tomoyuki Furuta et al. G3 2017;7:881-893 ©2017 by Genetics Society of America