BowTie 1 Inaccuracy 30 % ?

[Arupsss]

From BowTie Paper I found that, it is able to find exact matches and also in exact matches. Now, from bowtie manual, I found how to build index for a genomic database. So, I build it using command,

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.

[adaptivegenome]

Any reason you are.not using bowtie2?

[Arupsss]

Any reason you are.not using bowtie2?

I will use BWA, BoWtie 2 also to find a nice comparison ( I am just doing testing) . However, actually I want to know:

Is it possible to reach error of 30 % for BowTie 1 ? Or I am making some mistakes ?

[ffinkernagel]

Bowtie considers a 'N' in a read a mismatch - to quote the manual 'Ambiguous characters in the read mismatch all other characters.'

Depending on how you sampled the reads, that might explain 0 to 100% of your non matching reads.