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From TheGPMWiki
The coverage diagram is a graphical representation of the peptide coverage of a single identification of a protein. All coverage diagrams are scaled to be 600 pixels in length, regardless of the number of residues in the protein.
Below are two coverage diagrams for different identifications of the same protein, ENSP00000324804 (GPMDB).
Display Elements
- Red areas of the display are portions of the protein covered by peptides identified by the search software.
- Green areas are regions of the protein that are unlikely to be identified, due to conditions such as corresponding peptides being too long, too short or too hydrophobic. It is used as contextual evidence to assist users in determining of peptide coverage in an area of a protein is to be expected, or is indicative of a problem.
- The gray line is a visual element only.
Comparing Coverage Diagrams
Two areas of interest are numbered in both diagrams.
- A difference in detected peptide coverage can be seen between the top and bottom proteins above the area labeled with a 1; a peptide was detected in the bottom identification, but not the top.
- In the area labeled with a 2, a peptide was detected in the top identification, but not in the bottom, where it is coloured green to represent a low likelihood coverage by detectable peptides.
- Additionally, the difference in intensity between the red areas is a measure of reliability of the identification of the peptide at that point; the brighter the red, the lower the expect score for that peptide identification.