Analysis of copy number variants by three detection algorithms and their association with body size in horses

BMC Genomics

Table 7 Genome-wide associated CNVs for body size in horses

ECA	Start	End	Genome-wide (chromosome-wide) P value PennCNV	Genome-wide (chromosome-wide) P value QuantiSNP	Genome-wide (chromosome-wide) P value intersection of three detection programs	Copy number	Number of animals
1	156,012,982	156,870,455	0.006 (0.001)			1	111
1	156,657882	156,870,455		0.010 (0.003)		1	80
1	156,657,882	156,818,876			0.057 (0.018)	1	132
8	4,430,473	4,430,473	0.001 (0.001)		0.081 (0.023)	1	12/61
8	4,579,478	4,621,044		0.0002 (0.0002)		1	33
9	29,889,627	29,892,897		0.006 (0.001)		0, 1	37

The chromosome-wide (EMP1; in brackets) and genome-wide corrected significant P-values (EMP2) of the associated CNV regions detected by PLINK for the different algorithms and the number of animals showing a CNV in this region are given. For the intersection of three detection programs the P-value at the threshold of significance is displayed. CNVPartition did not show any significant association.

ISSN: 1471-2164