I am using a reference genome for mm10 mouse downloaded from NCBI, and would like to understand in greater detail the difference between lowercase and uppercase letters, which make up roughly equal parts of the genome. I understand that N is used for 'hard masking' (areas in the genome that could not be assembled) and lowercase letters for 'soft masking' in repeat regions.What does this soft masking actually mean? How confident can I be about the sequence in these regions?What does a lowercase n represent? 
Uppercase vs lowercase letters in reference genome
fasta;genome
What does this soft masking actually mean?A lot of the sequence in genomes are repetitive. Human genome, for example, has (at least) two-third repetitive elements.[1]. These repetitive elements are soft-masked by converting the upper case letters to lower case. An important use-case of these soft-masked bases will be in homology searches: An atatatatatat will tend to appear both in human and mouse genomes but is likely non-homologous.How confident can I be about the sequence in these regions?As you can be about in non soft-masked based positions. Soft-masking is done after determining portions in the genome that are likely repetitive. There is no uncertainty whether a particular base is 'A' or 'G', just that it is part of a repeat and hence should be represented as an 'a'.What does a lowercase n represent?UCSC uses Tandom Repeat Finder and RepeatMasker for soft-masking potential repeats. NCBI most likely uses TANTAN. 'N's represents no sequence information is available for that base. It being replaced by 'n' is likely an artifact of the repeat-masking software where it soft-masks an 'N' by an 'n' to indicate that portion of the genome is likely a repeat too.[1] http://journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1002384