Resequencing Alignments
This view compares sequences across strains of mouse and rat.
The first line of sequence is the reference genome. Subsequent lines of sequence are genomes for other samples or strains.
A vertical bar signifies we've got the same nucleotide in samples/strains as the reference sequence and genotype or read coverage data is availalbe to confirm that.
A dot means that we imply that the sample's sequence is the same as the reference at non-variant sites (i.e. the sequence between the variants with genotype calls). We don't have explicit data (either genotype or read coverage) to confirm this at the non-variant sites. We only have genotype calls at know variants sites (e.g. from the 1000 genomes project).
A tilde, or squiggle, signifies a lack of resequencing coverage at that position.
The alignment can be customised using the Configure this page option to show the actual nucleotide rather than a vertical bar or a dot. In the configuration window, select the matching basepairs option and show all. This will reveal the nucleotide sequence, instead of dots/vertical bars in positions that have the same sequence as the reference genome.
The sequence can also be marked-up with positions of exons, coding start and stop positions, and variations using Configure this page.
Options to mark-up the sequence include:
- Number of base pairs per row The number of base pairs per line can be varied (default 60 bps).
- Exons to highlight Exons on either or both strands may be displayed.
- Matching basepairs All nucleotides can be shown, or identical nucleotides in aligned sequences can be replaced with dots.
- Show variations SNPs (Single Nucleotide Polymorphisms) can be displayed along the sequences along with links to specific SNPView pages.
- Line numbering Select line numbering. Relative to this sequence starts from 1 for the region displayed, and relative to the coordinate system (shows the base pair position with respect to the chromosome).
- Codons Start and stop codons can be highlighted (in yellow) when exons are shown.
- Display pop-up information on mouseover Title tags can be switched on to show information about the feature when hovered-over with a mouse.
Example in mouse.