Resequencing alignments

Answer: 

This view compares sequences across individuals (human), breeds, or strains.

The first line of sequence is the reference genome. Subsequent lines of sequence are genomes for other individuals, breeds, or strains. A dot signifies the same nucleotide as the reference sequence at that position. The view can be customised to show the nucleotide rather than a dot (see next paragraph). A tilde, or squiggle, signifies a lack of resequencing coverage at that position.

Customise the page using the configure this page option. For example, select the matching basepairs option and show all. This will reveal the nucleotide sequence, instead of dots 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.