I sequenced DNA samples of a human being by using NGS technology and mapping reads (length is 90bp) to the human genome (version:hs37d5). Now I detected so low mapping rate (normal sample is higher than 99%, while my value is 88%). I collected all unmapped reads (243118 reads, flag of bam is 0) and tried to find their origins, while I can' t find any hits in NCBI nr database and only 2430 reads contained index sequences and only 210 reads containing adapter sequences.
So, my question is how should I do to find any reason which causes this low mapping rate? If you have some suggestions, please tell me.