Multi-breed genomic prediction using Bayes R with sequence data and dropping variants with a small effect

Table 6 Number of simulated QTL dropped or retained with their respective posterior inclusion probability (PIP)

Analysis	Drop	Dropped	PIP
Analysis	Drop	Dropped	0–0.01	0.01–0.05	0.05–0.1	0.1–0.2	0.2–0.5	0.5–1
FULL	0.0	0	3368	435	40	15	19	20
	0.7	2159	1179	463	35	19	19	23
	0.9	2981	293	520	36	24	18	25
CHR	0.0	0	3337	465	36	12	21	26
	0.7	2177	1164	460	36	14	20	26
	0.9	3025	306	461	42	15	19	29
KEPT	0.7	2177	1088	531	38	21	22	20
KEPT	0.9	3025	251	514	41	22	19	25
KEPT+	0.7	2177	1193	446	32	17	15	17
HD	0.9	3025	347	440	34	18	16	17

FULL = all variants analysed together, CHR = all variants analysed per chromosome, KEPT = variants selected by CHR reanalysed with all chromosomes together, KEPT + HD = variants selected by CHR and all HD variants reanalysed with all chromosomes together, drop = proportion of variants that are dropped after 10,000 MCMC iterations

ISSN: 1297-9686