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. 2018 Oct 10;562(7726):203–209. doi: 10.1038/s41586-018-0579-z

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© Springer Nature Limited 2018

Open Access This 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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Extended Data Fig. 1 — a–c, The three plots show heterozygosity and missing rates, which we used to flag poor quality samples (n = 488,377 samples). Panels a and b show heterozygosity for each sample before and after, respectively, correcting for ancestral background using principal components. The symbols (shapes and colours) indicate the self-reported ethnic background of each participant. Panel c shows the set of 968 samples we flagged as outliers (in red), and all other samples (in black), with shapes the same as for the other two plots. The vertical line shows the threshold we used to call samples as outliers on missing rate. In all plots missing rate data are transformed to the logit scale, but with the axis annotated with the original values.