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Table 2 Comparison between sequence- and array-called genotypes at corresponding positions

From: Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

Dataset Genotype concordance (%) Non-reference sensitivity (%) Non-reference discrepancy (%)
Raw 99.18 99.75 1.11
Filtered 99.19 99.77 1.09
Filtered & imputed 99.82 99.95 0.24