dbSNPs

Single Nucleotide Polymorphisms (SNPs) extracted from NCBI dbSNP. Clicking on the SNP provides links to the dbSNP SNP Report pages. Hovering over the SNP provides additional annotation including:

• Map weight - the number of times a SNP maps to the genome contig (range 1-10)
  
  • 1 = hit genome once, annotated on NT_ contigs
  • 2 = hit genome twice, annotated on NT_ contigs with warning
  • 3 = hit genome 3-9 times, not annotated
  • 10 = hit 10+ times on genome, not annotated
• Type - the genomic location of the SNP as defined at dbSNP. Defined as: Coding nonsynonymous (changes the amino acid/peptide); Coding synonymous (does not change the amino acid/peptide); in untranslated region; intronic (except first 2 and last 2 bases); in Splice-site (in first two or last two bases of intron); in locus region (not assigned to a gene but can be in an untranscribed region of a gene; may be in regulatory region).Users may be able to activate additional filters depending on whether the SNPS maps to a position
  (1)unique in contig or
  (2)more than one position in a contig another level of filtering that has been added allows users to also filter SNPS depending on the type of SNPS. Users can thus view a region as large as 5MB without loading the database.

dbSNPs are also colored depending on the type of SNP:

dbSNP Type	Color
Locus-region	Cadetblue
Intron	Red
5Upstream	LightPink
3Downstream	Orange
Synonymous Coding	Fuchsia
Non Synonymous Coding	Yellow
Splice-site	Dimgray
mRNA-UTR	Cyan
3UTR	Dark blue
5UTR	Light blue
near-gene-5	Peach
near-gene-3	Yellow Ochre
missense	Dark Chocolate
NA	Moss Green
Other	Black