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Table 1 Variants detected in 70 sequenced key ancestor animals

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

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