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Table 4 The variance components for each class across all traits when fitting the GRM simultaneously in the model.

From: Variance explained by whole genome sequence variants in coding and regulatory genome annotations for six dairy traits

Class

Fat (kg)

Milk (kg)

Protein (kg)

Fat Percent*

Protein Percent*

Fertility (calving interval, days)

AntisenseRNA

0 (0%)

0.69 (0%)

0 (0%)

0 (0%)

0 (0%)

1.63 (2.1%)

Long noncoding RNA

24.51 (15.5%)

12,041.50 (8.3%)

14.09 (13.6%)

0.14 (2.6%)

0.1 (8%)

3.67 (4.6%)

Splice Sites

15.85 (10%)

11,474.41 (8.0%)

6.21 (6%)

0.61 (11.3%)

0.13 (10%)

3.16 (4%)

Missense Deleterious

0 (0%)

0.69 (0%)

0 (0%)

0 (0%)

0 (0%)

0 (0%)

Missense Tolerated

0 (0%)

0.69 (0%)

0 (0%)

0 (0%)

0 (0%)

0 (0%)

3’ UTR

5.74 (3.6%)

6492.31 (4.5%)

7.78 (7.5%)

0.10 (1.9%)

0.08 (6%)

2.83 (3.6%)

5’ UTR

1.99 (1.3%)

3078.63 (2.1%)

2.80 (2.7%)

0.04 (0.7%)

0.002 (0.2%)

0.45 (0.6%)

miRNA Target Sites

11.07 (7.0%)

13,887.10 (9.6%)

10.78 (10.4%)

0.17 (3.2%)

0.1 (7%)

0 (0%)

TFBS

2.78 (1.8%)

874.09 (0.6%)

0.16 (0.2%)

0.01 (0.2%)

0.01 (0.7%)

3.97 (5%)

Upstream 5 k

12.85 (8.1%)

23,201.91 (16.1%)

21.37 (20.6%)

0.67 (12.6%)

0.22 (17.4%)

46.31 (58.6%)

Downstream 5 k

17.23 (10.9%)

11,835.03 (8.2%)

12.47 (12%)

0.01 (0.2%)

0.15 (11.5%)

0 (0%)

DNA Methylated

39.11 (24.8%)

26,529.43 (18.4%)

13.68 (13.2%)

2.51 (46.7%)

0.30 (24.2%)

3.65 (4.6%)

Synonymous

26.76 (16.9%)

34,816.95 (24.1%)

14.37 (13.9%)

1.11 (20.7%)

0.19 (15%)

13.35 (16.9%)

Error (Ve)

129.10

78,206.27

80.22

5.36

1.25

534.81

  1. In the brackets is the proportion of the total variance captured by variants in the class for the trait. The traits with an asterisk had their variance component multiplied by 100 since the values where too small to display in 2 decimal places. DNA methylated represents methylated regions in bovine placenta [23]. 3 prime and 5 prime untranslated regions (UTR) are represented as 3’ UTR and 5’ UTR, respectively. CDS represents the coding sequence of an exon. Transcription factor binding sites (TFBS) were from Bickhart D.M et al. [47]. Downstream 5 k and Upstream 5 k represent all variants that are found within 5 kilobases either upstream of a gene transcription start site (TSS) or downstream of a gene transcription termination site (TTS)