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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)