No PhyloP score for first stretch of chromosome?
I'm looking at phyloP data from UCSC (http://hgdownload.cse.ucsc.edu/goldenPath/mm9/phyloP30way/vertebrate/). It looks like the first 3 million bases or so of some chromosomes don't have phyloP scores. Example:
$ zcat chr1.phyloP30way.wigFix.gz | head -n 5
fixedStep chrom=chr1 start=3000306 step=1
0.223
0.240
...
so the start position is 3000306. Why are there no scores for position 1 through 3000305?
1 answer
From looking at the UCSC Genome Browser for mm9, say, along chr1, from bases 1 through 5M, it looks like protein-coding regions or gene transcript annotations (where conservation is measured) start a little past 3M bases. Here's a screenshot from the WashU Epigenome browser:
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