The size and composition of haplotype reference panels impact the accuracy of imputation from low-pass sequencing in cattle

Table 2 General overview of the haplotype reference panels: number of samples, coverage and number of variants called

Panel	Samples	Coverage	Variants	Biallelic SNPs	SNPs shared truth-query sets	Truth SNPs missing in haplotype panel	SNPs private to haplotype panel
BSW	150	9.40	22,493,568	19,682,362	13,537,126	317,806	6,145,236
BSW	75	9.65	19,883,488	17,345,201	13,373,462	481,470	3,971,739
BSW	30	9.42	17,035,514	14,839,600	12,810,541	1,044,391	2,029,059
Multibreed (50%)	150	10.48	27,710,504	24,325,185	13,568,744	286,188	10,756,441
Multibreed (25%)	150	10.86	28,755,400	25,266,484	13,531,721	323,211	11,734,763
Multibreed (10%)	150	11.44	28,608,506	25,126,433	13,427,451	427,481	11,698,982
Non-BSW	150	11.78	28,303,738	24,850,237	13,075,827	779,105	11,774,410
Non-BSW	75	11.78	25,059,239	21,968,792	12,868,909	986,023	9,099,883
Non-BSW	30	11.45	21,011,311	18,402,870	12,283,284	1,571,648	6,119,586

Shared and private variants are considered through exact matching (position and alleles). Values are the mean of 3 replicas per haplotype panel

ISSN: 1297-9686