About FishSNP

       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 13 farmed fish and two additional species (large yellow croaker and zebrafish) are currently undergoing updates. 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.

Datebase features


FishSNP is dedicated to cultivated fish species, with the latest update (Aug 2023) providing SNP information for 13 fish species. Two additional species, namely the large yellow croaker and zebrafish, are currently undergoing updates. These species have been prioritized based on their higher aquaculture production (FAO, 2021) and significance in fish research. 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.

Reliable SNP 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

General Statistics

August 2023




Last update

SNP number



Steps to get SNPs

The First Step

We collect the original sequencing data and genome version numbers of SNP articles about a certain species from pubmed

The Second Step

We process the raw data in a unified SNP calling ( GATK ) process to obtain the vcf file ( more detail in strategy part ).

The Third Step

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.

The Fourth Step

Perform snpEff processing on the obtained species SNP location information file to obtain the corresponding annotation file

Links to Resource

Links to SNP Resource :

More Links to Fish Resource :