Skip to main content

Table 1 Impact of SNPs 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 336790 16.308 %
5’-UTR premature start codon gain variant 36174 1.752 %
5’-UTR variant 220751 10.699 %
Initiator codon variant 52 0.003 %
Intergenic region 331008 16.028 %
Missense variant 431797 20.908 %
Missense variant + splice region variant 45 0.002 %
Splice regioin variant 1154 0.056 %
Splice region variant + synonymous variant 56 0.003 %
Start lost 323 0.016 %
Stop gained 3950 0.191 %
Stop gained + splice region variant 1 0 %
Stop lost 429 0.021 %
Stop retained variant 612 0.03 %
Synonymous variant 701868 33.985 %
  1. The polymorphisms 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 SNPs can be downloaded from the GigaTON website (ALL_SNP.oysterAssembly1.0_annot1.vcf)