Table 1. Iterative rounds of blended genome exome (BGE) development.

WES = whole exome sequencing, WGS = whole genome sequencing. Per-sample genotype concordance between deep whole genome variants and filtered Haplotype Reference Consortium (HRC) imputed variants from the low-pass genome, as described previously.⁸

Round	1	2	3	4	5	6 - Scaling
Blending ratio	67% WES + 33% WGS	67% WES + 33% WGS	60% WES + 40% WGS	40% WES + 60% WGS	33% WES + 67% WGS	33% WES + 67% WGS
Amount of Sequencing	96 samples on 1 lane NovaSeq S4	48 samples on 1 lane NovaSeq S4	48 samples on 1 lane of NovaSeq S4	48 samples on 1 lane of NovaSeq S4	64 samples on 1 lane of NovaSeq S4	768 samples on 2 lanes of NovaSeq S4
Coverage (mean)	29× WES 1.5× WGS	78× WES 2.55× WGS	78× WES 2.5× WGS	64.8× WES 3.7× WGS	37.7× WES 2.37× WGS	37× WES 2.5× WGS
% Exome bases ≥ 10×	96.33	98.34	98.27	98.18	96.44	96.37
% Exome bases ≥ 20×	75.09	97.84	97.79	97.19	87.04	84.08
Genotype concordance ${\text{R}}^2$ median (sd)	0.988 (1.56e-3)	0.991 (1.28e-3)	0.990 (2.90e-3)	0.995 (3.55e-2)	0.993 (1.15e-3)	0.993 (1.05e-3)