Table 5. Summary of the variants.

Variant type	Allele	Total	GATK-P	Phase-P	Imputation-P
The columns GATK-P, Phase-P (>0.8) and Imputation-P (>0.8) correspond to number of variants passing the respective filters. Multi allelic variants were dichtomized.
Indel	Biallelic	5,962,773	3,510,962	4,009,176	3,235,133
Indel	Non-biallelic	7,085,563	4,429,828	5,462,957	3,619,729
SNP	Biallelic	69,663,011	30,518,223	35,631,803	29,319,382
SNP	Non-biallelic	3,406,010	561,155	1,679,332	953,751
Total	Biallelic	75,625,784	34,029,185	39,640,979	32,554,515
Total	Non-biallelic	10,491,573	4,990,983	7,142,289	4,573,480