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Table 3 Predicted consequences of variants segregating in two lines. The table shows only the most sever consequence for a variant

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

Consequence type (most severe) Dam line Sire line
Splice donor variant 1396 1421
Splice acceptor variant 1126 1096
Stop gained 1615 1604
Frameshift variant 10,912 11,043
Stop lost 595 587
Start lost 423 421
Inframe insertion 990 987
Inframe deletion 1164 1186
Protein altering variant 62 62
Missense variant 70,758 69,983
Splice region variant 22,493 22,148
Incomplete terminal codon variant 12 11
Synonymous variant 76,977 75,279
Stop retained variant 149 135
Start retained variant 4 4
Coding sequence variant 98 96
Mature miRNA variant 12 16
5′ - UTR variant 168,000 164,866
3′ - UTR variant 348,135 344,514
Non-coding transcript exon variant 277,002 275,909
Intron variant 12,213,614 12,092,056
Non-coding transcript variant 11 10
Upstream gene variant 878,779 869,207
Downstream gene variant 757,364 750,548
Intergenic variant 8,942,362 8,848,730