Fig. 2

Assessment of imputation performance in the pipeline validation data set. Downsampling from 30× to 0.1× showed that lcWGS accuracy was above 0.90 r² for all samples at 0.5× (n = 4 independent random seeds for each sample and coverage value; error bars are 95% confidence intervals). The thick brown dashed line is a smoothed trendline of the average imputation quality while the thin gray dashed line demonstrates previously reported imputation quality from a genotyping array (r² = 0.90) [4]. AJ, Ashkenazi Jewish; CDX, Chinese Dai in Xishuangbanna, China; CEU, Utah residents with Northern and Western European ancestry; CHB, Han Chinese in Beijing, China; CLM, Colombians from Medellin, Colombia; GIH, Gujarati Indian from Houston, Texas; TSI, Toscani in Italia; YRI, Yoruba in Ibadan, Nigeria