Whole genome resequencing reveals an association of ABCC4 variants with preaxial polydactyly in pigs

BMC Genomics

Table 1 Genome association analysis and genotyping results of the top 10 SNPs

SNP ID	Pos (Ssc 10.2)	Region	Ref	Alt	GT_A (4)	GT_U (13)	CHISQ	P value
*rs791053563	*11:70808545*	*Intron*	G	C	*0/0 (4)*	*1/1 (11), 0/1(2)*	*25.11*	*5.422E-07*
rs709805150	11:42738578	IGR	C	T	1/1(3), 0/0(1)	0/0(13)	23.68	1.138E-06
*rs711914258	*11:71068779*	*Intron*	T	C	*1/1(4)*	*0/0(11), 0/1(1), 1/1(1)*	*21.87*	*2.911E-06*
*rs342954583	*11:71068862*	*Intron*	C	G	*1/1(4)*	*0/0(11), 0/1(1), 1/1(1)*	*21.87*	*2.911E-06*
*rs336503862	*11:71068919*	*Intron*	C	G	*1/1(4)*	*0/0(11), 0/1(1), 1/1(1)*	*21.87*	*2.911E-06*
rs320384943	11:70801220	Intron	T	C	1/1(4)	0/0(11), 1/1(2)	19.18	1.19E-05
*11:70439379	*11:70439379*	*Exon*	A	G	*1/1(4)*	*0/0(9), 0/1(4)*	*19.18*	*1.19E-05*
*11:71068754	*11:71068754*	*Intron*	A	G	*1/1(4)*	*0/0(10), 0/1(2), 1/1(1)*	*19.18*	*1.19E-05*
*rs335010523	*11:71068848*	*Intron*	T	A	*1/1(4)*	*0/0(10), 0/1(2), 1/1(1)*	*19.18*	*1.19E-05*
*rs325300849	*11:71068895*	*Intron*	A	G	*1/1(4)*	*0/0(10), 0/1(2), 1/1(1)*	*19.18*	*1.19E-05*

Pos Physical position, Ssc Sus scrofa, Ref Reference allele, Alt Altered allele, GT_A Genotypes of cases, GT_U Genotypes of controls; The number “0” represent reference allele and “1” represent altered allele; The number behind the genotype in brackets represent the number of this genotype’s individuals; CHISQ: Basic allelic test chi-square (1df); P: Asymptotic p-value for this test; IGR Intergenic region. The bold italic highlighted rows (*) represent the SNPs which identified by genome scanning (Additional file 5: Table S5)

ISSN: 1471-2164