Characterization of a haplotype-reference panel for genotyping by low-pass sequencing in Swiss Large White pigs

BMC Genomics

Table 1 Variants detected in 70 sequenced key ancestor animals

	Raw	Filtered & imputed	Dam line	Sire line
Number of animals	70	70	32	38
Sequence coverage¹	16.69 (8.72–36.85)	16.69 (8.72–36.85)	18.02 (9.31–36.85)	15.57 (8.72–27.73)
Number of variants
All	28,407,060	26,862,369	24,358,047	24,093,052
Biallelic SNP	22,191,375	21,209,725	19,456,000	19,232,692
Biallelic INDEL	4,379,470	4,339,947	3,960,976	3,928,684
Others²	1,836,215	1,312,697	941,071	931,676
Autosomal variants
All	27,582,843	26,198,587	23,774,053	23,531,919
Biallelic SNP	21,553,323	20,715,354	19,015,058	18,808,294
Biallelic INDEL	4,248,742	4,211,012	3,846,008	3,817,622
Others²	1,780,778	1,272,221	912,987	906,003

¹ estimated from the autosomes
² this category contains multi-allelic SNP, multi-allelic INDEL, as well as sites that may contain both SNP and INDEL

ISSN: 1471-2164