Any difference between capital letter(ATGC) and lowercase letter(atgc) in hg19 fasta file

Question

[Chen Sun]

I find that in hg19 fasta file, the sequence contains capital letters(ATGC) and lowercase letters(atgc), so I am wondering is there any difference between these 2 kinds of letters, or is there any special meanings?

Answer 1

[Pierre Lindenbaum]

See http://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/

Repeats from RepeatMasker and Tandem Repeats Finder (with period of 12 or less) are shown in lower case; non-repeating sequence is shown in upper case.

[Devon Ryan]

I'll add that the term for this is "soft masking" (as opposed to "hard masking", wherein these bases would simply be replaced by Ns).