bowtie-build hg19.fa hg19
Now, I want to run a query read file named "a493081_1.fastq" to find exact and inexact matches (allowing 1,2 and 3 substitutions - as specified in BowTie paper) for 150 bps read length.
So, I issue the command
./bowtie --all -v 0 hg19 a493081_1.fastq a.txt
to find all alignments with 0 mismatch. And BowTie outputs,
# reads processed: 200000 # reads with at least one reported alignment: 145692 (72.85%) # reads that failed to align: 54308 (27.15%) Reported 173932 alignments to 1 output stream(s)
However, all reads are taken from hg19, so BowTie should give output "NO reads that failed to align". BowTie provides inaccurate matching, but near about 30 % inaccuracy is not similar as I found from various comparison. Can anybody help me, in what reasons this inaccuracy can happen or any procedure to make it more accurate.
Additional: I should mention, my fastq file contains 150 bps single end reads.