A joint use of pooling and imputation for genotyping SNPs

BMC Bioinformatics

Table 1 Markers counts and proportions on the LD and the HD maps per MAF bin

MAF	0.00–0.02	0.02–0.04	0.04–0.06	0.06–0.10	0.10–0.20	0.20–0.40	0.40–0.50	Total
LD map (counts)	520	779	673	1537	3969	6561	2976	17015
HD map (counts)	12775	5235	2823	4766	9009	12613	5476	52697
LD map (%)	0.987	1.478	1.277	2.917	7.532	12.450	5.647	32.288
HD map (%)	24.242	9.934	5.357	9.044	17.096	23.935	10.392	100

The counts are given in the two first rows of the table, the proportions in the two last ones. The proportions are given relatively to the total number of SNPs on the HD map. The HD map is on the whole 3 times denser than the LD map but the density is not uniformly increased over the MAF bins. Almost 25% of the markers on the HD map are very rare variants (\(MAF < 0.02\)), that is 25 times denser than on the LD map where they represent less than 1% of the markers

ISSN: 1471-2105