Table 2. Imputation performance.

Metric	PRIMAL, Cross-Validation	PRIMAL WGS Variants	PRIMAL+LD WGS Variants
# Variants imputed	53,861	7,008,666	7,008,666
# Samples	1,317	1,317	1,317
Concordance	99.8 ±. 01%	-	99.3%*
Het concordance	99.8 ±. 01%	-	99.3%*
Phasing rate	99.6 ±. 01%	99.4%	99.4%
Allele call rate	91.4 ± 8%	91.6%	95.1%
Genotype call rate	75.5 ± 14%	76.2%	87.3%
PO assignment rate	80.0 ± 15%	80.0%	83.0%

PRIMAL and PRIMAL combined with LD-based imputation (PRIMAL+LD) performance and calls rates for the 1,317 Hutterites whose genomes were not sequenced. The concordance and het concordance figures marked by asterisks were based on the concordance of the PRIMAL and LD-based imputation on the set of genotypes called by both. Cross-validation SNVs were chosen from the framework SNVs as explained in the text.