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Table 2 Impact of INDELs on the GigaTON protein set

From: GigaTON: an extensive publicly searchable database providing a new reference transcriptome in the pacific oyster Crassostrea gigas

TYPE (alphabetical order) Count Percent
3’-UTR variant 32867 35.312 %
5’-UTR variant 12890 13.849 %
Chromosome number variation 15 0.016 %
Disruptive in-frame deletion 968 1.061 %
Disruptive in-frame insertion 502 0.539 %
Frameshift variant 5653 6.074 %
Frameshift variant + start lost 156 0.168 %
Frameshift variant + stop gained 84 0.09 %
Frameshift variant + stop lost 51 0.055 %
In-frame deletion 430 0.462 %
In-frame insertion 369 0.396 %
Intergenic region 39050 41.955 %
Start lost + disruptive in-frame deletion 3 0.003 %
Start lost + in-frame deletion 7 0.008 %
Start lost + in-frame insertion 1 0.001 %
Stop gained + disruptive in-frame deletion 1 0.001 %
Stop gained + disruptive in-frame insertion 1 0.001 %
Stop gained + in-frame insertion 7 0.008 %
Stop lost + in-frame deletion 1 0.001 %
  1. The INDELs have been annotated using snpEff v4.15 [22] using the transdecoder open reading frame annotations made on the contigs. The complete annotated vcf files for INDELs can be downloaded from the GigaTON website (ALL_INDEL.oysterAssembly1.0_annot1.vcf)