Plotting distribution of allelic frequency under different coverage values

[toots]

I'm new to bioinformatics, and have an incomprehensible PI. Could someone clue me in on some of what is going on in the prompt below? For instance:
1) What's "LD"?
2) What do the different coverage values signify? How do I implement that in R?
3) I have no idea what the RefAlleleCount, etc. bit means. Aren't all of those ratios the same anyhow?

I realize I'm asking really broad, noobish questions, but a little context would be reeeaaally helpful. Thanks.

" RNAseq reads covered 5,000 biallelic human autosomal SNPs (all are heterogeneous, assume they are not in LD). Please write simple R statements to plot the distribution of the alternative allelic frequency under sequencing coverage 2x, 5x, 10x, 20x, respectively. Also calculate the p-values with the hypothesis that there are no differential allelic expression for these three SNPs: (RefAlleleCount:AltAlleleCount) 1:4, 2:8, 4:16. "

Edit: I've discovered that LD is linkage disequilibrium. Still fairly lost though.

[chadn737]

1) LD = Linkage Disequalibrium
2) Coverage refers to the number of reads covering each bp
3) RefAlleleCount = # of reads with the reference allele, AltAlleleCount = # reads with an alternative allele (i.e. not matching the reference).

[toots]

Is there actually enough information in that prompt to do an analysis in R? I don't even know which "three SNPs" are being referred to. Is that implicit somehow?