Skip to main content

Table 4 Proportion of annotated SNP in genomic regions and mutation types

From: Sequence imputation from low density single nucleotide polymorphism panel in a black poplar breeding population

   Value % (number)
   SNPchip SNPseq
Region variant hit
  downstream 2,43 (183) 6,23 (12338)
  exonic 36,18 (2728) 14,96 (29607)
  intergenic 3,78 (285) 32,28 (63901)
  intronic 37,02 (2791) 30 (59377)
  splicing 0,04 (3) 0,1 (192)
  exonic; splicing 0 (0) 0,001 (3)
  upstream 1,8 (136) 5,71 (11307)
  UTR3 8 (603) 6,3 (12470)
  UTR5 3,55 (268) 3,02 (5968)
  UTR5; UTR3 0 (0) 0,01 (20)
  upstream; downstream 0,6 (45) 1,18 (2340)
Annotated Positions 93,4 (7042) 99,79 (197523)
Total number of Positions 100 (7540) 100 (197932)
Mutation type
  frameshift deletion 0 (0) 0,12 (246)
  frameshift insertion 0 (0) 0,06 (118)
  Non-frameshift deletion 0 (0) 0,08 (159)
  Non-frameshift insertion 0,01 (1) 0,04 (84)
  synonymous SNV 19,09 (1439) 6,64 (13133)
  Non-synonymous SNV 16,92 (1276) 7,85 (15534)
  Stop gain 0,15 (11) 0,15 (299)
  Stop loss 0,01 (1) 0,02 (35)
Total number of exonic positions 36,18 (2728) 14,96 (29608)
  1. Annotation results for SNPchip and SNPseq in percentage of counts per annotation category, and number of corresponding positions in brackets. For region variant hit: exonic;splicing corresponds to a variant within exon region but close to exon/intron boundary; UTR5;UTR3 corresponds to a variant positioned where two coding regions overlapped, one in forward and one in reverse; upstream;downstream corresponds to a variant positioned in an intergenic region between two neighbouring genes