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The file size upload limit for a document is 50mb by default but is it file size of the document or file size of document on disk.

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Can you elaborate on why this information is relevent? Why not just bump the allotment to a larger size plus a healthy margin for error? Does your SQL store have modified clustering? –  Ray Nov 7 '12 at 17:51
    
The difference is minuscule, but it is based on the file size not file size on the disk. –  Hossein Aarabi Nov 7 '12 at 18:49
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up vote 1 down vote accepted

After comparing disk space, to site collection (Adding removing a site collection) The quota is based on the actual file sizes.

To get the site collection totals:

$site = Get-SPSite http://sitecollection
$site.Usage.Storage;
$site.Dispose();
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There's isn't any big difference at all as said by Hossein Aarabi but limit is for file size not file size on disk as far as I find out by research however couldn't find any reference.

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