. 2017 Aug 24;207(2):489–501. doi: 10.1534/genetics.117.300198

Table 5. Predictive ability in categorical models (mean ± SE).

Data sets	Traits	$C M$	$C E$	$C_{H} M$	$C_{H} E$	$C_{H} M \| G A$	$C_{H} E \| G A$	$C_{H} M \| G A$ ^a	$C_{H} E \| G A$ ^*
Mouse	W6W	0.493 ± 0.002	0.516 ± 0.002	0.519 ± 0.002	*0.551 ± 0.002*	0.498 ± 0.002	0.524 ± 0.002	0.501 ± 0.002	0.525 ± 0.002
	W7W	0.497 ± 0.002	0.519 ± 0.002	0.527 ± 0.002	*0.550 ± 0.002*	0.502 ± 0.002	0.528 ± 0.002	0.504 ± 0.002	0.528 ± 0.002
	W8W	0.512 ± 0.002	0.527 ± 0.002	0.525 ± 0.001	*0.543 ± 0.001*	0.515 ± 0.002	0.533 ± 0.002	0.517 ± 0.002	0.533 ± 0.002
	W10W	0.477 ± 0.002	0.494 ± 0.002	0.491 ± 0.002	*0.511 ± 0.002*	0.473 ± 0.002	0.494 ± 0.002	0.479 ± 0.002	0.497 ± 0.002
	GSL	0.394 ± 0.001	0.404 ± 0.001	0.403 ± 0.001	*0.414 ± 0.001*	0.394 ± 0.001	0.404 ± 0.001	0.396 ± 0.001	0.406 ± 0.001
	BMI	0.190 ± 0.003	0.199 ± 0.003	0.186 ± 0.003	0.203 ± 0.003	0.208 ± 0.002	*0.216 ± 0.002*	0.207 ± 0.002	0.215 ± 0.002
	BL	0.239 ± 0.002	0.248 ± 0.002	0.244 ± 0.002	0.252 ± 0.002	0.249 ± 0.002	*0.257 ± 0.002*	0.248 ± 0.002	0.255 ± 0.002
	%B220+	0.544 ± 0.002	0.559 ± 0.002	0.534 ± 0.002	0.556 ± 0.001	0.541 ± 0.002	0.558 ± 0.002	0.545 ± 0.002	*0.560 ± 0.002*
	%CD3+	0.523 ± 0.003	*0.530 ± 0.003*	0.518 ± 0.003	0.523 ± 0.003	0.518 ± 0.003	0.527 ± 0.003	0.523 ± 0.003	0.529 ± 0.003
	%CD4+	0.486 ± 0.001	0.494 ± 0.001	0.478 ± 0.001	0.488 ± 0.001	0.482 ± 0.001	0.492 ± 0.001	0.491 ± 0.001	*0.498 ± 0.001*
	%CD8+	0.707 ± 0.001	0.712 ± 0.001	0.700 ± 0.001	0.699 ± 0.001	0.722 ± 0.001	*0.728 ± 0.001*	0.721 ± 0.001	*0.728 ± 0.001*
	%CD4+/CD3+	0.651 ± 0.001	0.655 ± 0.001	0.654 ± 0.001	0.650 ± 0.001	0.674 ± 0.001	*0.678 ± 0.001*	0.674 ± 0.001	*0.678 ± 0.001*
	%CD8+/CD3+	0.684 ± 0.001	0.686 ± 0.001	0.680 ± 0.001	0.674 ± 0.001	0.706 ± 0.001	*0.709 ± 0.001*	0.706 ± 0.001	*0.709 ± 0.001*
	CD4+/CD8+	0.682 ± 0.001	0.685 ± 0.001	0.678 ± 0.001	0.674 ± 0.001	0.703 ± 0.001	*0.707 ± 0.001*	0.703 ± 0.001	*0.707 ± 0.001*
	CD4Intensity	0.574 ± 0.002	0.582 ± 0.002	0.569 ± 0.002	0.580 ± 0.002	0.569 ± 0.002	0.579 ± 0.002	0.578 ± 0.002	*0.586 ± 0.002*
	CD8Intensity	0.413 ± 0.002	0.443 ± 0.002	0.442 ± 0.002	*0.485 ± 0.002*	0.409 ± 0.003	0.444 ± 0.002	0.412 ± 0.002	0.443 ± 0.002
DGRP	E2 (F)	0.201 ± 0.010	0.201 ± 0.010	0.211 ± 0.010	0.198 ± 0.011	*0.225 ± 0.010*	0.212 ± 0.011	0.208 ± 0.010	0.192 ± 0.011
	E2 (M)	0.026 ± 0.010	0.028 ± 0.010	0.040 ± 0.010	0.038 ± 0.009	*0.045 ± 0.009*	0.043 ± 0.009	0.039 ± 0.011	0.039 ± 0.012
	1-hexanol (F)	0.184 ± 0.010	0.188 ± 0.010	0.193 ± 0.009	0.199 ± 0.009	*0.222 ± 0.009*	0.221 ± 0.009	0.220 ± 0.010	0.219 ± 0.010
	1-hexanol (M)	0.234 ± 0.009	0.235 ± 0.009	0.235 ± 0.009	0.233 ± 0.009	*0.254 ± 0.008*	0.247 ± 0.008	*0.254 ± 0.008*	0.246 ± 0.009
Rice	DS_PH	0.486 ± 0.007	0.483 ± 0.007	0.497 ± 0.007	0.484 ± 0.006	*0.523 ± 0.007*	0.517 ± 0.007	*0.523 ± 0.007*	0.517 ± 0.007
	DS_FLW	0.534 ± 0.005	0.536 ± 0.005	0.556 ± 0.005	0.556 ± 0.005	0.567 ± 0.005	*0.570 ± 0.005*	0.567 ± 0.005	0.569 ± 0.005
	DS_YLD	0.289 ± 0.006	0.301 ± 0.006	0.285 ± 0.006	0.313 ± 0.006	0.325 ± 0.005	*0.340 ± 0.005*	0.324 ± 0.005	*0.340 ± 0.005*
	WS_PH	0.482 ± 0.006	0.487 ± 0.006	0.496 ± 0.005	0.500 ± 0.005	0.518 ± 0.005	*0.521 ± 0.005*	0.518 ± 0.005	*0.521 ± 0.005*
	WS_FLW	0.467 ± 0.007	0.476 ± 0.007	0.487 ± 0.006	0.500 ± 0.006	0.504 ± 0.006	*0.513 ± 0.006*	0.503 ± 0.006	*0.513 ± 0.006*
	WS_YLD	0.258 ± 0.007	0.288 ± 0.007	0.241 ± 0.007	0.302 ± 0.007	0.275 ± 0.008	*0.314 ± 0.008*	0.275 ± 0.008	*0.314 ± 0.008*
	Mean accuracy	0.432	0.441	0.438	0.449	0.447	0.457	0.448	0.456

For the DGRP data set, two traits for which the gene-annotation-based models show improved predictive ability are presented. W6W–W10W, body weight at 6–8 and 10 weeks; GSL, growth slope between 6 and 10 weeks of age; BMI, body mass index; BL, body length; %B220+, percentage of B220 cells; %CD3+, percentage of CD3 cells; %CD4+, percentage of CD4 cells; %CD8+, percentage of CD8 cells; %CD4+/CD3+, percentage of CD4 and CD3 cells; %CD8+/CD3+, percentage of CD8 and CD3 cells; CD4+/CD8+, ratio of CD4 to CD8 cells; CD4Intensity, CD4inCD3XGeoMean; CD8Intensity, CD8inCD3YGeoMean. F, female; M, male. DS, dry season; WS, wet season; PH, plant height; FLW, flower time; YLD, grain yield. For each trait (row), the values in boldface indicate the best prediction among all models and values in italic are those significantly higher than $C M$ (P < 0.05, pairwise t-test).

Indicates models including gene-based haplotypes and unmapped SNPs simultaneously.