Table 2

Annotation of SNPs in the Quarter Horse genome

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


Doan et al. BMC Genomics 2012 13:78   doi:10.1186/1471-2164-13-78

Open Data