I am trying to understand the information present in PhastCons elements bed files from USCS Table Browser. Following the information I found [here][1] I managed to get a description of the column names, but not a description of what they are measuring. I checked other BioStars posts, and apparently, the PhastCons have scores that range from 0-100, but this is not true according to the description from Table Browser (see below):

![enter image description here][2]

I also checked the distribution of the the "score" column, and on the file that is available to download, the smallest score is 117. So I am assuming the phastConsElements46wayPrimates bed file only contains the conserved regions. Is this correct? Also, where can I get a description of what the LOD score is measuring here.

 [1]: http://hgdownload.cse.ucsc.edu/goldenPath/hg19/database/?C=M;O=A
 [2]: /media/images/1aae92a6-1ed5-46f1-bb9b-01cb4d6f
Hello,

We offer more information in the track description (https://genome.ucsc.edu/cgi-bin/hgTrackUi?db=hg19&c=chrX&g=cons46way).

There's 4 components to our conservations tracks:

- A multiz alignment of the sequences
- Basewise conservation as predicted by phyloP - this is displayed as a wiggle track
- Element conservation as predicted by phastCons - this is also displayed as a wiggle, but less resolution than the phyloP
- Conserved elements as predicted by phastCons with the --viterbi option (I believe this is now --most-conserved, it used to be viterbi: http://compgen.cshl.edu/phast/phastCons-tutorial.php) - this is discrete elements in bed format, which is the file you are looking at

Below is the description of that specific track. lod stands for "log-odds score", and the score is ultimately transformed to be between 0-1000 to optimize the Genome Browser's display.

> The conserved elements were predicted by running phastCons with the
> --viterbi option. The predicted elements are segments of the alignment that are likely to have been "generated" by the conserved state of the
> phylo-HMM. Each element is assigned a log-odds score equal to its log
> probability under the conserved model minus its log probability under
> the non-conserved model. The "score" field associated with this track
> contains transformed log-odds scores, taking values between 0 and
> 1000. (The scores are transformed using a monotonic function of the form a * log(x) + b.) The raw log odds scores are retained in the
> "name" field and can be seen on the details page or in the browser
> when the track's display mode is set to "pack" or "full".

If you have any follow up questions, our public help desk can always be reached at genome@soe.ucsc.edu. You may also send questions to genome-www@soe.ucsc.edu if they contain sensitive data. For any Genome Browser questions on Biostars, the UCSC tag is the best way to ensure visibility by the team.