Fig. 9
From: Imputation strategies for genomic prediction using nanopore sequencing
Genotype concordance for genotypes derived from low-coverage Oxford Nanopore Technologies (ONT) sequence data imputed using GLIMPSE and QUILT. Twelve animals were sequenced twice at two separate time points and genotypes were calculated separately for each of the sequencing runs. Five different sequencing coverages were evaluated for the two different imputation methods as well as five different imputation reference panel sizes. The largest imputation reference panel used 48 million SNP, a minor allele frequency (MAF) cutoff of 0.1, 0.2 and 0.3, was used to subset the 48 million SNP reference panel down. The final imputation reference panel used only the 700Â k SNP in the bovine HD SNP array