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)