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Extended Data Fig. 1

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Summary of sample-based quality control.

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.

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