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.


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.


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.