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. 2016 Jun 13;6(8):2553–2561. doi: 10.1534/g3.116.027730

Table 3. Reliabilities and observed and prediction reliability factors for different sets of markers.

ncaus Train Val Set Reliability Heritability RFO RFP
50 JER RDC Cc 0.85 (0.02) 0.79 (0.01) — —
PSEQ1kb 0.38 (0.03) 0.75 (0.01) 0.45 (0.04) 0.39 (0.02)
PSEQ10kb 0.27 (0.03) 0.72 (0.01) 0.31 (0.04) 0.25 (0.02)
PSEQ25kb 0.13 (0.02) 0.71 (0.01) 0.15 (0.03) 0.16 (0.01)
P50K 0.04 (0.01) 0.78 (0.01) 0.05 (0.02) 0.03 (0.00)
P50KC 0.09 (0.02) 0.54 (0.02) 0.11 (0.02) 0.20 (0.01)
PHD 0.08 (0.02) 0.78 (0.01) 0.10 (0.03) 0.03 (0.00)
PHDC 0.31 (0.04) 0.61 (0.02) 0.36 (0.04) 0.34 (0.02)
RDC JER Cc 0.95 (0.01) 0.78 (0.01) — —
PSEQ1kb 0.47 (0.04) 0.70 (0.01) 0.50 (0.04) 0.38 (0.02)
PSEQ10kb 0.26 (0.03) 0.66 (0.02) 0.28 (0.04) 0.23 (0.02)
PSEQ25kb 0.13 (0.03) 0.61 (0.02) 0.14 (0.03) 0.14 (0.01)
P50K 0.09 (0.02) 0.75 (0.01) 0.10 (0.02) 0.02 (0.00)
P50KC 0.14 (0.03) 0.39 (0.02) 0.15 (0.03) 0.18 (0.01)
PHD 0.14 (0.03) 0.77 (0.01) 0.15 (0.03) 0.02 (0.00)
PHDC 0.40 (0.04) 0.51 (0.03) 0.42 (0.04) 0.33 (0.02)
100 JER RDC Cc 0.84 (0.01) 0.79 (0.01) — —
PSEQ1kb 0.36 (0.03) 0.79 (0.01) 0.43 (0.03) 0.43 (0.02)
PSEQ10kb 0.24 (0.03) 0.79 (0.01) 0.29 (0.03) 0.26 (0.01)
PSEQ25kb 0.08 (0.01) 0.78 (0.01) 0.09 (0.01) 0.17 (0.01)
P50K 0.06 (0.01) 0.79 (0.01) 0.07 (0.01) 0.05 (0.00)
P50KC 0.09 (0.02) 0.61 (0.01) 0.11 (0.02) 0.21 (0.01)
PHD 0.11 (0.02) 0.79 (0.01) 0.13 (0.02) 0.06 (0.00)
PHDC 0.28 (0.03) 0.68 (0.01) 0.34 (0.03) 0.37 (0.01)
RDC JER Cc 0.92 (0.01) 0.79 (0.01) — —
PSEQ1kb 0.47 (0.04) 0.75 (0.01) 0.50 (0.04) 0.41 (0.02)
PSEQ10kb 0.32 (0.03) 0.72 (0.01) 0.35 (0.03) 0.24 (0.01)
PSEQ25kb 0.12 (0.02) 0.68 (0.01) 0.13 (0.02) 0.14 (0.01)
P50K 0.07 (0.01) 0.76 (0.01) 0.08 (0.01) 0.03 (0.00)
P50KC 0.14 (0.02) 0.47 (0.01) 0.15 (0.02) 0.19 (0.01)
PHD 0.14 (0.02) 0.78 (0.01) 0.15 (0.02) 0.03 (0.00)
PHDC 0.37 (0.04) 0.59 (0.01) 0.40 (0.04) 0.36 (0.01)
250 JER RDC Cc 0.73 (0.02) 0.79 (0.01) — —
PSEQ1kb 0.26 (0.02) 0.81 (0.01) 0.35 (0.03) 0.47 (0.01)
PSEQ10kb 0.12 (0.01) 0.80 (0.01) 0.17 (0.02) 0.32 (0.01)
PSEQ25kb 0.04 (0.01) 0.81 (0.01) 0.06 (0.01) 0.23 (0.01)
P50K 0.04 (0.01) 0.79 (0.01) 0.05 (0.01) 0.13 (0.00)
P50KC 0.07 (0.01) 0.74 (0.01) 0.09 (0.02) 0.27 (0.01)
PHD 0.05 (0.01) 0.79 (0.01) 0.07 (0.01) 0.13 (0.00)
PHDC 0.20 (0.02) 0.76 (0.01) 0.27 (0.03) 0.41 (0.01)
RDC JER Cc 0.85 (0.01) 0.79 (0.01) — —
PSEQ1kb 0.33 (0.03) 0.77 (0.01) 0.39 (0.04) 0.42 (0.01)
PSEQ10kb 0.19 (0.03) 0.75 (0.01) 0.22 (0.03) 0.27 (0.01)
PSEQ25kb 0.07 (0.01) 0.71 (0.01) 0.08 (0.02) 0.17 (0.01)
P50K 0.08 (0.02) 0.76 (0.01) 0.09 (0.02) 0.07 (0.00)
P50KC 0.11 (0.02) 0.60 (0.01) 0.13 (0.02) 0.22 (0.01)
PHD 0.10 (0.02) 0.78 (0.01) 0.11 (0.02) 0.07 (0.00)
PHDC 0.25 (0.03) 0.66 (0.01) 0.29 (0.03) 0.38 (0.01)

SE of reliability, estimated heritability, RFO and RFP are given in parentheses. ncaus, the number of causative mutations; train, training population; val, validation population; set, markers used for prediction; RFO, observed reliability factor; RFP, predicted reliability factor; JER, Jersey; RDC, Danish Red; Cc, causative mutations; PSEQ1/10/25kb, sequence interval on 1 kb/10 kb/25 kb of the causative mutations; P50K and PHD, all markers on the 50K and HD SNP chip, respectively; P50KC and PHDC, the closest causative mutations to each 50K and HD marker, respectively.