Fig. 1
From: Developing a 670k genotyping array to tag ~2M SNPs across 24 horse breeds
Comparing high QUAL genotypes called de-novo to the SNP50 array in Morgans and Standardbreds. SNPs on chromosome (ECA1) 1 with genotype calls from both WGS and SNP50 array were ranked by decreasing QUAL score for Morgans (MOR) at 6X (3759 SNPs; 12 individuals) and 12X (3751 SNPs; 6 individuals) coverage, and Standardbreds (STD) at 6X (4422 SNPs; 5 individuals) and 12X (4380 SNPs; 3 individuals) coverage. The cumulative proportion of genotypes that agree between platforms was compared based on ranking de-novo variants by QUAL score. Variants with missing data on either platform were excluded