SNP id

Note: the custom ids of FishSNP begin with "FS", and followed by three numbers which are corresponding to species (as shown in figure above) , the rest numbers are serial numbers. Notably, we also provide SNP annotation, visualization and flanking sequence extraction for zebrafish and Larimichthys crocea from the EVA database from the EVA database. Paramisgurnus dabryanus, currently there is no mature annotation file, all can only be searched by "advance search", and the id assigned by the FishSNP database (FS013XXXXXX, see the related download vcf on the download page)

SNP Search

Note: two ways can be employed to search data, one is simple search, searching by typing in SNP ID or gene name, and the other is 'advanced' hyperlink , which switch to a new search page that provide chromosome interval and genome version selection.

SNP Dispaly List

Note: the search result list shows all matching SNPs related to the search term, we provide part information of SNPs, according to which target SNP can be selected.

Basical information

Note: basical information include SNP ids(costume ids or EVA ids), organism, genome version(genome ids from various resoures), position (chromosome : location), alleles (ref/alt), variation type, annotation (obtained by snpEff), publication (the source of the data), and P-value(Mendelian segregation test or Hardy Weinberg equilibrium test).Users can also download the detail information of SNPs by clicking the button "download all information" and the file is saved in XML Spreadsheet 2003 file format which can be opened by Excel or other softwares.

Flanking sequence

Note: Users can seclect genome version and length of flanking sequence, and target SNP is in the middle of sequence which marked by square brackets.

Multiple Genomes

Note: The annotation of this locus on other genomes can be clicked on the content of other genomes in this part, and the content of the annotation information is the same as the Annotation part.

Annotation

• Allele (or ALT): In case of multiple ALT fields, this helps to identify which ALT we are referring to
• Annotation (a.k.a. effect): Annotated using Sequence Ontology terms. Multiple effects can be concatenated using '&'.
• Putative_impact: A simple estimation of putative impact / deleteriousness : {HIGH, MODERATE, LOW, MODIFIER}
• Gene Name: Common gene name (HGNC). Optional: use closest gene when the variant is "intergenic".
• Feature type: Which type of feature is in the next field (e.g. transcript, motif, miRNA, etc.). It is preferred to use Sequence Ontology (SO) terms, but 'custom' (user defined) are allowed.
• Transcript biotype: The bare minimum is at least a description on whether the transcript is {"Coding", "Noncoding"}. Whenever possible, use ENSEMBL biotypes.
• Rank / total: Exon or Intron rank / total number of exons or introns.
• HGVS.c: Variant using HGVS notation (DNA level)
• HGVS.p: If variant is coding, this field describes the variant using HGVS notation (Protein level). Since transcript ID is already mentioned in 'feature ID', it may be omitted here.
• Errors, Warnings or Information messages: Add errors, warnings or informative message that can affect annotation accuracy
• more explain

Populations

Note:the table inculdes type(family represents family populations, random represents random populations), project(sequence data resources), location(where the population was sampled), sequenceing type, P value( Mendelian separation ratio test or Hardy Weinberg test), allele(ref and alt frequency) and genotype freq(GA|GG: indicate parental genotype, the rest show the proportion of different genotypes).

Publications

Note: the detail information of article which is the data resources.

Vatiation View

Note: users can select different genome versions to browse target SNPs and the distribution of nearby SNPs and click on the SNP sites of interest to obtain basic information.

Annotate

Note: This is an example that demonstrates how to use the annotation tool step by step. Follow the sequence from top to bottom: Step 1: Fish Species and Genomes Selection,in this section,click on "Select Species" to choose the desired species. Then click on "Select Genome" to choose the available genome version corresponding to the selected species. Step 2: Annotation,in this section, upload the required SNP information. There are two ways to upload it: directly copy and paste the SNP positions, and upload a VCF file.Then choose which parts you want to display and hide in the result file.Step 3: Results,in this section, provide your correct email information. We will send the results to your email. After that, click on "Submit" to initiate the submission.
Result Interpretation: The results are divided into two sections: Result in FishSNP Section:if the requested SNP positions are already included in our database, they will be displayed here. You can click on the respective result box to view the corresponding information. Annotation Result Section:if the requested SNP positions are not included in our database, they will be annotated based on the selected genome version. Please note that if the number of annotated positions exceeds 500, the computation time might be longer. In order to ensure a smooth user experience, we will send the related results to your email.

Download

Note: Users can get all SNP data of different species by clinking button 'download', including the VCF file of all SNP loci under the specific genome version of each species and unmapping data which means the original SNP information is not aligned to any genome version for SNP data from attachment.