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Table 1 Comparison of GVs annotated with CooVar and VEP for human individual HG00732-200-37-ASM

From: CooVar: Co-occurring variant analyzer

  CooVar VEP
Runtime 36m 37h 24m
Total reported GVs 4,158,840 4,043,939
 Intronic/intergenic/UTR 4,133,885 4,019,490
 Impacting protein-coding exon 24,955 24,449
  Synonymous/stop retained 11,585 11,434
  Missense 12,011 11,576
   Conservative (%)$ 9,526 (79.3) 7,447 (64.3)
   Non-conservative (%)+ 2,485 (20.7) 2,110 (18.3)
   Unknown consequence (%) 0 (0) 2,019 (17.4)
  Splice donor/acceptor 97 184
  Stop lost 47 46
  Stop gained 137 134
  Frameshift 470 490
  Inframe 199 165
  Other 0 31
  Multiple* 409 389
ORF disrupted 782¥ 871§
  1. Each GV reported by CooVar (v0.05) and VEP (v2.6) was assigned to one (and only one) of the above categories. $ CooVar: Grantham score conservative or moderately conservative; VEP: SIFT benign; + CooVar: Grantham score moderately radical or radical; VEP: SIFT deleterious. * GVs assigned to more than one category due to differential impact on different transcripts. ¥ Presence of internal stop codon within the first 70% of ORF length, after applying all variants. § Predicted frameshift or stop gain variant within the first 70% of ORF length. Abbreviations: GV … genomic variation; ORF … open reading frame; VEP… Variant Effect Predictor; UTR… untranslated region.