There are six subtracks of this track: four for single-nucleotide mutations, one for each base, showing all possible substitutions, one for insertions and one for deletions. All subtracks show the CADD Phred score on mouseover. Zooming in shows the exact score on mouseover, same basepair = score 0.0.
PHRED-scaled scores are normalized to all potential ~9 billion SNVs, and thereby provide an externally comparable unit for analysis. For example, a scaled score of 10 or greater indicates a raw score in the top 10% of all possible reference genome SNVs, and a score of 20 or greater indicates a raw score in the top 1%, regardless of the details of the annotation set, model parameters, etc.
++The four single-nucleotide mutations tracks have a default viewing range of +score 10 to 50. As explained in the paragraph above, that results in +slightly less than 10% of the data displayed which helps visualization. The +deletion and insertion tracks have a default filter of 10-100 since they +display discrete items and not graphical data. +
Single nucleotide variants (SNV): For SNVs, at every
genome position, there are three values per position, one for every possible
nucleotide mutation. The fourth value, "no mutation", representing
the reference allele, e.g. A to A, is always set to zero.
When using this track, zoom in until you can see every basepair at the
top of the display. Otherwise, there are several nucleotides per pixel under
your mouse cursor and instead of an actual score, the tooltip text will show
the average score of all nucleotides under the cursor. This is indicated by
the prefix "~" in the mouseover. Averages of scores are not useful for any
application of CADD.