Fig. 4.

Accuracy of genotyping by low-coverage sequencing. a Concordance between array-called and sequence-called genotypes at 46,001 biallelic autosomal SNP in 243 pigs that had been sequenced at either low (N = 175; < 1.5-fold) or medium to high (N = 68; 8.88–37.60-fold) coverage. Correlations of (b) diagonal (r = 0.96) and (c) off-diagonal (r = 0.99) elements of genomic relationship matrices constructed from array- and GLIMPSE-called genotypes at 44,268 SNP that had minor allele frequency > 0.01