Ensembl SNPs
Single Nucleotide Polymorphisms (SNPs) extracted from
Ensembl SNP. IDs beginning with rs are SNPs from
NCBI dbSNP. SNPs that are discovered by Ensembl from resequencing and comparing reads to the genome assembly have Ensembl SNP IDs beginning with ENSRNOSNP. Clicking on the SNP links to the Ensembl 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
- Alleles - the alleles observed for the SNP and submitted to Ensembl
- Ambiguity Code - the IUPAC nucleotide ambiguity code representing the polymorphism as identified by Ensembl
- Strain - the strains in which the SNP was identified
- Type - the genomic location of the SNP as defined at Ensembl. Defined as: Flanking to a transcript (within 5,000 bp upstream or downstream from the transcript); in a UTR; intronic; or in a coding sequence. Coding SNPs are divided into those annotated by Ensembl as being synonymous (does not change the amino acid/peptide) or non-synonymous (changes the amino acid/peptide).
Ensembl SNPs are colored as following:
| Ensembl SNP Type | Color |
|---|
| Intergenic | Cadetblue |
| Intron | Red |
| Upstream | LightPink |
| Downstream | Orange |
| Synonymous Coding | Fuchsia |
| Non Synonymous Coding | Yellow |
| Splice-site | Dimgray |
| mRNA-UTR | Cyan |
| 3 Prime UTR | Dark blue |
| 5 Prime UTR | Light blue |
| Stop gained | Peach |
| Stop Lost | Yellow Ochre |
| NA | Moss Green |
| Other | Black |
.