Table 2.

Summary of single-nucleotide polymorphisms in horses.

Category	Count	Percentage	Note
Sample size	N = 48	—	“Splice_region” means that a variant is within 2 bp of a splice junction. “Splice_acceptor” means that the variant hits a splice acceptor site (defined as 2 bases before the exon start site, except for the first exon). “Splice_donor” means that the variant hits a splice donor site (defined as 2 bases after the end of the coding exon, except for the last exon). “Upstream/downstream” means that a variant overlaps with the 1-kb region upstream/downstream of the gene end site. The number of effects is larger than the number of SNPs because a variant can be annotated for 2 or more effects.
SNP	15 341 213	—
3_prime_UTR	172 656	0.46
5_prime_UTR	46 446	0.13
Downstream	2 488 567	6.70
Intergenic_region	10 032 903	27.02
Intragenic	794	0.00
Intron	10 441 311	28.12
Missense	103 427	0.28
Non_coding_transcript_exon	96 876	0.26
Non_coding_transcript	10 793 318	29.07
Splice_acceptor	384	0.00
Splice_donor	577	0.00
Splice_region	25 231	0.07
Start_lost	283	0.00
Stop_gained	1054	0.00
Stop_lost	224	0.00
Stop_retained	82	0.00
Synonymous	129 097	0.35
Upstream	2 474 202	6.66
Exon	327 360	0.88
No. of effects	37 134 791	100