Skip to main content

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

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

Analysis Drop Dropped PIP
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
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
  1. 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
\