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

Table 1 Impact of SNPs on the GigaTON protein set

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 %

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)

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