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Table 2 Annotation of SNPs in the Quarter Horse genome

From: Whole-Genome sequencing and genetic variant analysis of a quarter Horse mare

  Total Homozygous Heterozygous Novel Ensembl Genes
All SNPs 3,157,093 1,293,374 1,863,719 2,814,367 24,023
   Intergenic 2,224,292 908,169 1,316,123 1,991,041 19,644
   Intergenic (Upstream w/in 1 kb) 40,948 19,241 21,707 37,566 12,803
   Intergenic (Downstream w/in 1 kb) 31,901 13,327 18,574 28,494 10,580
   Intergenic (Up/Down w/in 1 kb) 929 427 502 866 399
   Genic 859,023 352,210 506,813 756,400 19,414
Intron 811,204 332,455 478,749 712,764 14,778
Non-Coding Exon 5,935 2,019 3,916 5,575 2,123
5' UTR 1,734 1,014 720 1,630 1,049
3' UTR 1,821 780 1,041 1,594 1,184
Intron Splice Site 300 185 115 280 276
Exon Splice Site 657 320 337 593 595
Coding Exon 37,372 15,437 21,935 33,964 10,485 (305 imprinted)
Synonymous 19,667 7,626 12,041 17,699 7,982
Stop Gain 214 50 164 206 190
Stop Loss 8 5 3 7 8
Non-Synonymous 18,140 8,076 10,064 16,645 6,899
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