Table 1.

Significantly segregating genome-wide variants identified in OAAM1 included 6 single nucleotide variants (SNVs) and one 2.7-kb deletion.

Variant	Ref allele	Alt allele	OAAM1 genotype	SNPEFF	Public database (.bam files)			Ensembl transcript ID
					Homo Alt allele	Het Alt allele	Breeds
chr9:82 287 859	G	A	AA (WGS) AG (Sanger)	HIGH Nonsense	0	0	N/A	ENSECAT00000012645
chr20:27 996 691	T	C	CC	MODERATE Missense	0	5	Franches-Montagnes Standardbred Unspecified	ENSECAT00000022878
chr25:28 840 158	G	A	AA	MODERATE Missense	0	3	Icelandic Norwegian Fjord	ENSECAT00000016101
chr7:24 869 230	C	T	TT	MODERATE Missense	0	2	Haflinger Franches-Montagnes	ENSECAT00000005230
chr7:65 101 509	T	G	GG	MODERATE Missense	0	9	German Warmblood Haflinger Unspecified Franches-Montagnes Aedigenberger	ENSECAT00000007397
chr8:29 207 931	T	G	GG	MODERATE Missense	0	4	Franches-Montagnes Friesian dwarf Standardbred Norwegian Fjord	ENSECAT00000020160
chr18:54 616 748– 54 619 464		Del	Del/Del	N/A	0	0	N/A	Intergenic (HOXD4/3)

Of these, five were identified in the heterozygote state in other breeds as determined by publically accessible 121 mapped genomes of Equus caballus within the Sequence Read Archive database (SRA; https://www.ncbi.nlm.nih.gov/sra). This dataset included two Arabian horses. One SNV (chr9:82 287 859) was unique to OAAM1 and predicted to result in a nonsense mutation in ZNF707 (ENSECAT00000012645) but was found to be a heterozygous variant via Sanger sequencing.

Alt, alternate; Het, heterozygous; Homo, homozygous; Ref, reference; WGS, whole-genome sequencing.