Off topic: FastQC results with abnormal GC content and Overrepresented sequences in RIP-seq datasets

Question

[yoyostudents5775]

my mouse RIP-seq data have abnormal GC content and the fastqc result in 'GC content' have 2 peaks, first one is about 55% in x axis, y axis is about 500000. the second one as about 85% in axis,y axis is about 1600000, very sharp peak.besides, the GC content each base is not about 25% for A,T,G,C. they looks like electrocardiogram from 0bp to 150 bp. the overrepresented sequence almost G and C. I checks the unmaapped reads in my bam files and blast with NCBI nr database, which shows that these reads were come from mouse. I think it isn't the contaminate with other sequence, I really can't find how this can be? Many thanks for your help~