Evaluation of approaches for identifying population informative markers from high density SNP Chips

Wilkinson, Samantha; Wiener, Pamela; Archibald, Alan L; Law, Andy; Schnabel, Robert D; McKay, Stephanie D; Taylor, Jeremy F; Ogden, Rob

doi:10.1186/1471-2156-12-45

BMC Genomic Data

Table 4 Power of assignment in individual breeds

From: Evaluation of approaches for identifying population informative markers from high density SNP Chips

		Delta				pairwise Wright's F_ST				pairwise W&C's F_ST				PCA
Breed	Markers	log0	log1	log2	log3	log0	log1	log2	log3	log0	log1	log2	log3	log0	log1	log2	log3
Angus	50	100	79.17	66.67	33.33	85.4	64.58	43.75	18.75	93.8	81.25	37.5	16.67	85.4	68.75	52.08	20.83
	100	100	91.67	77.08	72.92	97.9	91.67	89.58	87.5	100	100	95.83	91.67	89.6	79.17	77.08	60.42
	200	100	100	100	100	100	100	100	100	100	100	97.92	97.92	100	97.92	97.92	97.92
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	100	97.92	97.92
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Brown Swiss	50	100	95.8	95.8	95.8	100	100	100	95.8	100	100	100	91.7	100	100	100	100
	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	200	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Charolais	50	72	56	24	0	92	76	60	24	92	60	44	16	88	68	20	4
	100	88	76	56	24	96	96	84	60	96	88	80	44	92	92	84	52
	200	96	96	96	92	96	96	92	92	96	96	96	92	96	96	92	84
	300	100	96	96	96	96	96	96	92	96	96	96	96	96	96	96	96
	400	100	96	96	96	96	96	96	96	96	96	96	96	96	96	96	96
Finnish Ayrshire	50	100	60	20	10	100	90	60	40	70	70	60	50	100	100	70	40
	100	100	100	90	90	100	90	80	50	90	90	80	50	100	100	100	80
	200	100	100	100	100	100	100	100	80	100	100	100	90	100	100	100	100
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Guernsey	50	100	100	95.2	95.2	95.2	95.2	95.2	95.2	100	95.2	95.2	95.2	95.2	95.2	95.2	95.2
	100	100	100	100	95.2	100	100	100	100	100	100	100	100	95.2	95.2	95.2	95.2
	200	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Hereford	50	68	60	36	24	92	80	60	48	100	92	84	68	96	88	76	72
	100	100	88	88	84	100	100	96	84	100	100	100	96	100	100	100	100
	200	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Holstein	50	96	72	48	24	92	72	64	40	96	96	96	96	96	96	88	84
	100	100	96	96	92	100	100	100	100	100	100	92	88	100	100	92	92
	200	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Jersey	50	100	100	100	92.9	100	100	100	100	100	100	100	100	100	100	100	96.4
	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	200	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Limousin	50	92	84	56	40	96	92	84	48	88	80	72	44	84	60	20	12
	100	100	100	96	76	100	92	88	84	88	88	72	72	92	92	72	48
	200	100	100	100	100	100	100	100	96	92	92	92	92	100	100	100	100
	300	100	100	96	96	100	96	96	96	96	96	96	92	100	100	100	100
	400	100	100	100	100	100	96	96	96	100	96	96	96	100	100	100	100
Norwegian Red	50	90.5	71.4	61.9	33.3	90.5	71.4	57.1	28.6	90.5	81	71.4	57.1	85.7	76.2	61.9	28.6
	100	100	95.2	90.5	85.7	95.2	90.5	85.7	76.2	90.5	90.5	76.2	71.4	95.2	95.2	90.5	85.7
	200	100	100	100	100	100	100	100	95.2	100	100	100	95.2	95.2	100	100	95.2
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Piedmontese	50	100	94.7	94.7	78.9	100	100	100	94.7	100	94.7	94.7	73.7	94.7	84.2	73.7	47.4
	100	100	100	100	94.7	100	100	100	100	100	100	100	100	94.7	94.7	94.7	68.4
	200	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Red Angus	50	93	73.3	46.7	26.7	86.7	53.3	33.3	20	80	53.3	46.7	13.3	93.3	53.3	46.7	20
	100	93	80	66.7	60	86.7	86.7	80	66.7	100	93.3	93.3	73.3	93.3	80	73.3	60
	200	93	93.3	93.3	93.3	100	100	100	93.3	100	100	93.3	93.3	100	93.3	80	80
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	86.7	86.7	86.7
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	93.3	93.3	93.3
Red Poll	50	88.9	88.9	83.3	72.2	100	100	83.3	77.8	94.4	88.9	77.8	66.7	100	94.4	94.4	94.4
	100	100	100	100	100	100	100	100	94.4	100	100	100	100	100	100	100	100
	200	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100
Shorthorn	50	80	76	68	56	92	92	92	80	92	92	92	88	96	92	80	80
	100	92	88	88	88	92	92	92	88	96	96	92	92	100	96	96	92
	200	96	96	92	92	100	96	96	96	100	96	96	96	100	100	100	100
	300	96	100	100	100	100	96	96	96	100	96	96	96	100	100	100	100
	400	100	100	100	96	100	100	100	100	100	100	100	100	100	100	100	100
Simmental	50	100	92	68	36	92	92	80	60	96	84	68	40	88	68	44	32
	100	100	92	84	80	96	100	96	96	100	100	88	76	92	92	76	56
	200	100	100	100	96	100	100	100	100	100	100	96	92	92	88	76	68
	300	100	100	100	96	100	100	100	100	100	96	96	96	96	92	88	76
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	96	92
Welsh Black	50	100	100	93.3	76.7	96.7	93.3	83.3	80	100	96.7	90	83.3	96.7	96.7	90	83.3
	100	100	100	100	100	96.7	93.3	93.3	93.3	100	100	100	100	96.7	96.7	96.7	96.7
	200	100	100	100	100	100	100	100	100	100	100	100	96.7	100	100	96.7	96.7
	300	100	100	100	100	100	100	100	100	100	100	100	100	100	96.7	96.7	96.7
	400	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100	100

Percentage of individuals that were successfully assigned to their breed origin, at the 4 stringency threshold levels, for each selection method.

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ISSN: 2730-6844

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