9c70d91534dd8366a57c563718c715308d3dac78 gperez2 Mon Jun 21 16:03:47 2021 -0700 Code review edits, shorting longLabel’s within 80 characters, refs #27743 diff --git src/hg/makeDb/trackDb/human/caddSuper.html src/hg/makeDb/trackDb/human/caddSuper.html index b2230c6..977a825 100644 --- src/hg/makeDb/trackDb/human/caddSuper.html +++ src/hg/makeDb/trackDb/human/caddSuper.html @@ -19,31 +19,32 @@ CADD scores strongly correlate with allelic diversity, pathogenicity of both coding and non-coding variants, experimentally measured regulatory effects, and also rank causal variants within individual genome sequences with a higher value than non-causal variants. Finally, CADD scores of complex trait-associated variants from genome-wide association studies (GWAS) are significantly higher than matched controls and correlate with study sample size, likely reflecting the increased accuracy of larger GWAS.

Display Conventions and Configuration

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.

+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.

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.