Table 2.

WGS Variants Identified in 30x Coverage of a Persian Cat PRA Trio

	Analysis type†
Variant*	WGS trio	Trio Segregation	Retnet genes	GWAS haplotype
SNP	14,215,442	487,324	74,852	9607
MNP	822,020	11,856	4214	644
Insertion	1,390,990	16,656	7439	636
Deletion	1,279,028	22,134	6760	663
Mixed	304,341	3314	1588	198
Total	18,011,821	541,284	94,853	11,748

*Each alternate allele identified during variant calling is considered separately for tabulation of variant types, using the definitions at http://snpeff.sourceforge.net/SnpEff_manual.html#eff. ^†The analyses are based on feline reference genome sequence (V6.2). The GWAS identified an associated haplotype on cat chromosome E1. For Trio Segregation, the variants segregated with the disease phenotype as well, not just parent to offspring