From fig it looks the quality of your sequence is not good. Currently u are throwing out most of your data by trimming. 410775 is too little reads to push to bowtie.

First check if you have primers/adapters attached to beginning/end of sequence. If so, remove them. Look at over-represented sequence, take few of those, blat them to genome individually and see what portion of the sequence maps and what doesn't. That should give you idea about primer/adapter sequence.

Or trim the last 5 or 10 nucleotide, and analyze how mapping differs ? compare with different parameters of trimming. You need to play a bit with your data.

Bowtie is not very tolerant of low-quality reads. If you want to use this data, I'd suggest aligning with BBMap, and using the raw untrimmed reads.