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What is "unmasked genome(%)" ? - (Dec/22/2012 )

Dear all,

I read a paper, 'Amplification free illumina sequencing-library ...' by Kozarewa.
Figure 2 in this paper, y axis is denoted as 'unmasked genome(%)' and x axis is depth of genome base coverage.
I guess the number of certain base according to coverage follows Poisson distribution, but I don't know what the relationship with "'unmasked genome(%)" is.
Simply, 'unmask' what?

Thank you.


If you have used BLAST search, you may find that repetitive sequence in your input is replaced by "n"s, this is called masking. So masked genome means genome with repetitive sequence excluded because repetitive sequences from deep seq data that match to more than one location are usually ignored.