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Coordinates Of Ucsc Table Tracks?

I just downloaded the UCSC mapability track for the mm9 genome (based on the link here: http://www.mail-archive.com/genome@soe.ucsc.edu/msg02504.html) and I found that on chromosome 1, the first entries start at position 3000000. I am wondering why the program was not run on the earlier part of chromosome 1? Am I misunderstanding the coordinate notation? It seems like the mapability track should begin on chromosome 1, coordinate 0 (since it's 0-based indexing.) Any ideas?

thanks.

ucsc genome sequence genome
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updated by Biostar Biostar • written by User 9996 User 9996

2 answers

Mouse chromosomes are acrocentric and thus the first 3Mb are masked with Ns. Consequently, annotations don't begin until ca. position 3,000,000.

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written by Aaronquinlan Aaronquinlan

It seems that the mouse genome is acrocentric. The first bases only contains some 'N'.

curl -s "http://hgdownload.cse.ucsc.edu/goldenPath/mm9/chromosomes/chr1.fa.gz" |\
  gunzip  -c | cat -n 
 1  >chr1
 2  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 3  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 4  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 5  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 6  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 7  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 8  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
 9  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
10  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
(...)
60001  NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
60002 Gaattcttttctatgatttagtttaatatgttttctgggtgtttcagct
(...)
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updated by Ram Ram • written by Pierre Lindenbaum Pierre Lindenbaum

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