Marker imputation error on 254 breeding lines in the Cycle 29 Semi-Arid Wheat Screening Nursery. For each of 250 randomly chosen markers from the full set of 34,749 genotyping-by-sequencing (GBS) markers, 25 genotypes were masked and the imputed genotypes were compared to observed. Panel A shows imputation error at different levels missing data. The colors indicate what fraction of the 254 genotypes was missing before masking the 25 additional genotypes. The upper and lower limits for the range of different of missing data for different tests are shown in the legend. In panel B, results are shown as a function of the minor allele frequency. The median (column height) and first and third quartile (error bars) statistics are shown for four imputation methods: (i) heterozygote (het), (ii) population mean, (iii) multivariate normal expectation maximization (EM), and (iv) random forest (RF) regression.