I have whole genome sequencing data, single end read.
I am using the Ghr38 reference
To align with bowtie2, I did the indexing
but always get a super low alignment rate. any ideas or recommendations on what to do?

(wgs) ubuntu@cm-wgs:~/block_storage/ReferenecGenomebowtie2$ bowtie2 -x GRCh38 -U ~/storage/C98/3922Normal.fastq -S ./local3922Normal.sam –local -p 30
653127208 reads; of these:
653127208 (100.00%) were unpaired; of these:
565456872 (86.58%) aligned 0 times
11416699 (1.75%) aligned exactly 1 time
76253637 (11.68%) aligned >1 times
13.42% overall alignment rate

without local alignment the alignment percentage was 1.5%