Uppercase vs lowercase letters in reference 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