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.