|
Trait
|
Data
|
Analysis
|
DropProp
|
Number of variants per distribution
|
|---|
|
0 \(\sigma_{g}^{2}\)
|
0.0001 \(\sigma_{g}^{2}\)
|
0.001 \(\sigma_{g}^{2}\)
|
0.01 \(\sigma_{g}^{2}\)
|
|---|
|
Milk
|
HD
|
FULL
|
0
|
627,503
|
4299
|
22
|
10
|
|
S
|
KEPT
|
0.9
|
483,521
|
6603
|
17
|
6
|
|
S + HD
|
KEPT + HD
|
0.9
|
1076,643
|
8927
|
22
|
6
|
|
Fat
|
HD
|
FULL
|
0
|
627,510
|
4312
|
9
|
4
|
|
S
|
KEPT
|
0.9
|
483,614
|
6307
|
7
|
4
|
|
S + HD
|
KEPT + HD
|
0.9
|
1080,078
|
8890
|
9
|
3
|
|
Prot
|
HD
|
FULL
|
0
|
627,347
|
4476
|
9
|
3
|
|
S
|
KEPT
|
0.9
|
482,957
|
6352
|
8
|
3
|
|
S + HD
|
KEPT + HD
|
0.9
|
1078,647
|
9025
|
9
|
2
|
|
Fert
|
HD
|
FULL
|
0
|
625,899
|
5668
|
260
|
8
|
|
S
|
KEPT
|
0.9
|
548,382
|
5715
|
310
|
5
|
|
S + HD
|
KEPT + HD
|
0.9
|
1135,712
|
10,569
|
436
|
7
|
- Prot = protein, fert = fertility, HD = HD genotypes used for prediction, S = sequence variants used for prediction, FULL = all variants analysed together, KEPT = variants selected per chromosome reanalysed with all chromosomes together, KEPT + HD = variants selected per chromosome and all HD variants reanalysed with all chromosomes together, dropProp = proportion of variants dropped after 10,000 MCMC iterations, \(\sigma_{g}^{2}\) = additive genetic variance
