Genetics Selection Evolution

Table 3 SNPs detected using different P-value thresholds in the discovery population, the non-discovery population, and in all 3549 samples

From: Genomic prediction based on selective linkage disequilibrium pruning of low-coverage whole-genome sequence variants in a pure Duroc population

Trait	Population	P-value thresholds
Trait	Population	0.0001	0.0003	0.0005	0.0007	0.001	0.003	0.005	0.007	0.01
AGE	Discovery	105	1300	2994	5158	9052	27,662	43,604	62,631	94,385
	Non-discovery	319	1588	4281	7093	11,312	31,880	54,720	79,016	103,418
	All	343	2273	5152	6686	8537	28,082	49,399	73,167	108,976
BF	Discovery	4342	6403	7591	9236	12,033	32,926	54,589	73,302	101,580
	Non-discovery	8711	15,582	20,086	23,274	27,369	44,655	60,946	79,791	106,278
	All	12,624	16,895	19,203	21,012	23,068	40,461	59,719	77,576	105,749
TTN	Discovery	2774	7079	12,726	17,925	22,400	43,547	63,641	80,742	107,811
	Non-discovery	5733	11,605	15,370	19,011	23,697	47,462	64,705	83,287	111,884
	All	12,343	20,169	23,003	25,560	29,767	54,070	74,004	92,246	116,156

SNPs with a P-value lower than each threshold were selected for each trait. Non-discovery means the samples include 2108 training and 441 validation samples
AGE age to 100 kg live weight, BF back fat thickness, TTN total teat number

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ISSN: 1297-9686

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