3.2 Output formats

3.2.1 Figures

Manhattan plot

Fig. Manhattan plot by GWAS

Scatter plot: Q-Q plot

Fig. Q-Q plot by GWAS

Histogram: GEBV distribution

Fig. Distribution for GEBVs

Density function: Accuracies for GS validations

Fig. Distribution for prediction accuracies

Scatter plot: GS predictions against observations

Fig. Distribution for prediction accuracies

Histogram: Heterozygosity distribution

Fig. Histograms for overview of heterozygosity

Phenotype overview

Fig. Figure for overview of phenotypes

3.2.2 Tabular results

GWAS report

TABLE 3.10: Tabular GWAS results

SNP	Chromosome	Position	P.value	maf	effect
PZB00859.1	1	157104	0.8796673	0.2402135	0.0513818
PZA01271.1	1	1947984	0.0450554	0.4893238	0.5985480
PZA03613.2	1	2914066	0.0152657	0.2900356	0.7550551
PZA03613.1	1	2914171	0.7736487	0.2508897	-0.1049524
PZA03614.2	1	2915078	0.1072168	0.4697509	-0.4744598

GS: GEBV

TABLE 3.11: GEBV for each individual

taxa	GEBV
ID_1	-1.77193474724802
ID_2	1.72387204220987
ID_3	1.68334659084122
ID_4	-2.41038775121833
ID_5	-5.74618607007748
…	…

GS: Marker effects

TABLE 3.12: Genetic effects for each marker

V1	u
M_1	-0.00567222219641276
M_2	0.0212495891997373
M_3	0.030552733100474
M_4	-0.0212824623926987
M_5	-0.0126398188395629
…	…

GS: Validation results

TABLE 3.13: Accuracies from GS validation

r	rmse	trait	iter	fold
0.6141	5.8551	y75	1	1
0.5466	5.0126	y75	1	2
0.6173	4.7957	y75	1	3
0.5112	5.8834	y75	1	4
0.5525	4.5914	y75	1	5

GS: Predicted values

TABLE 3.14: List of predicted and observed phenotypes

obs	pre	trait	iter	fold
-1.2619	-2.8336	y75	1	1
2.5937	-0.1296	y75	1	2
-7.4122	-0.6723	y75	1	3
-4.3864	-3.1929	y75	1	4
-3.9676	-7.8634	y75	1	5
-8.4040	-2.2128	y75	2	1
-4.4187	-4.3261	y75	2	2
16.0423	1.9852	y75	2	3