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Table 3 Results of functional annotation by VEP

From: Construction of a large collection of small genome variations in French dairy and beef breeds using whole-genome sequences

Functional class All SNP InDels
3′ UTR variant 70,139 61,080 9059
5′ UTR variant 14,899 13,696 1203
Frameshift variant 2287 0 2287
Inframe deletion 814 0 814
Inframe insertion 358 0 358
Splice acceptor variant 649 510 139
Splice donor variant 1471 1378 93
Start lost 169 169 0
Stop gained 1159 1139 20
Stop lost 68 67 1
Mature miRNA variant 171 135 36
Intron variant 8,446,403 7,513,594 932,809
Downstream gene variant 1,335,987 1,179,502 156,485
Intergenic variant 18,568,837 16,664,272 1,904,565
  1. This table summarizes the functional classification of all variants reported in this study