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Table 4 Number of SNPs and INDELs annotated using the VEP software per region and assembly

From: Investigating the impact of reference assembly choice on genomic analyses in a cattle breed

 

ARS-UCD1.2

UOA_Angus_1

 

SNPs

INDELs

SNPs

INDELs

Exonic regions (%)

224,549 (1.15)

11,561 (0.40)

262,775 (1.35)

16,391 (0.58)

Intronic regions (%)

6,365,765 (32.55)

992,015 (33.84)

8,185,503 (42.09)

1,236,006 (43.47)

Intergenic regions (%)

12,966,725 (66.30)

1,927,646 (65.76)

10,998,370 (56.56)

1,590,860 (55.95)

  1. Annotated SNPs and INDELs are classified by region where detected. The total number of annotated variants per assembly and region are displayed here. The table lists only the most severe annotation. The percentage of variants placed in each region per variant type and assembly is shown between parentheses
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