Genetics Selection Evolution

Table 2 Number of SNPs per chromosome in the 50K, 3K and 7K SNP panels and the accuracy of imputation based on 3K and 7K panels with PLSR and Beagle

From: Use of partial least squares regression to impute SNP genotypes in Italian Cattle breeds

	Number of SNP				Imputation accuracy (PLSR)		Imputation accuracy (Beagle)
Chromosome	50K	3K	7K		3K	7K	3K	7K
1	2814	146	320		0.916	0.953	0.876	0.919
2	2294	119	277		0.911	0.951	0.863	0.922
3	2191	107	261		0.897	0.944	0.846	0.898
4	2123	106	237		0.903	0.941	0.861	0.908
5	1812	107	233		0.912	0.948	0.872	0.912
6	2164	109	254		0.908	0.953	0.867	0.914
7	1876	95	215		0.908	0.949	0.858	0.915
8	2026	104	232		0.919	0.953	0.872	0.915
9	1708	92	214		0.904	0.949	0.851	0.909
10	1841	97	209		0.909	0.946	0.872	0.915
11	1913	91	222		0.901	0.947	0.862	0.914
12	1408	85	175		0.903	0.942	0.856	0.899
13	1486	75	166		0.910	0.949	0.860	0.911
14	1453	70	166		0.897	0.945	0.850	0.912
15	1427	74	167		0.898	0.945	0.864	0.915
16	1337	74	160		0.910	0.950	0.864	0.913
17	1367	65	156		0.888	0.936	0.842	0.900
18	1147	59	136		0.877	0.924	0.825	0.884
19	1164	56	143		0.878	0.935	0.827	0.895
20	1351	70	172		0.921	0.960	0.886	0.933
21	1170	58	134		0.881	0.934	0.832	0.899
22	1087	57	133		0.894	0.941	0.849	0.900
23	919	47	118		0.887	0.938	0.842	0.895
24	1072	54	135		0.888	0.941	0.842	0.903
25	831	41	109		0.865	0.926	0.816	0.887
26	905	45	102		0.889	0.931	0.841	0.890
27	834	41	100		0.872	0.924	0.832	0.890
28	806	46	99		0.871	0.922	0.826	0.879
29	901	47	110		0.875	0.934	0.828	0.888
Total SNP	43427	2237	5155	Mean	0.896	0.942	0.851	0.905

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