Fish SNP database is the first web-based, open source, free and continuously updated fish SNP database ( FishSNP ) for all fishes. At present, millions of high-quality non-redundant snps have been identified from 12 farmed fish. The database has three main functions: SNP tag search, detailed information browsing and SNP and flanking sequence download. Some gadgets are integrated into FishSNP to visualize and analyze data.
The Fish SNP focus on cultured fishs, the most recent update ( Dec2021 ) includes SNP information for twelve fish species which have higher aquaculture production ( FAO,2021 ). We will collect SNP information of all cultured fishs in the furture.
The database provides each fish species with different genome vesions and corresponding annotation information.
The database collects the original sequencing data of the fish family, unified standard filtering, and uses the family family to perform Mendelian separation ratio to detect the progeny data to obtain reliable SNP information
We collect the original sequencing data and genome version numbers of SNP articles about a certain species from pubmed
We process the raw data in a unified SNP calling ( GATK ) process to obtain the vcf file ( more detail in strategy part ).
We first collect family data for a species, perform Mendelian separation ratio detection on the SNP position information obtained in the second step, and filter out sites that do not conform to the law.
Perform snpEff processing on the obtained species SNP location information file to obtain the corresponding annotation file