Bowtie vs Bowtie2

[beajorrin]

I'm doing my PhD in Genomics of the interaction rhizobium-legume.
I've sequenced 100 bacteria pooled with Illumina Hiseq 2000, 500 bp PE library, 100 bp reads, and I obtained 12 millions of reads. I've trimmed the reads in the 3' end with Trimmomatic. Then I've analysed my data with Bowtie and Bowtie2, but I've got different results between them, but not those that appear in the article Langmead & Salzberg, 2012, Fast Gapped-read alignment with Bowtie2. Nature Methods 9(4):357-359.
( http://www.nature.com/nmeth/journal/...meth.1923.html )

The options that I've used are:

Bowtie 2: --phred64 --very-sensitive --end-to-end -M2 -I0 -X1000 --fr --no-discordant --no-contain --no-overlap -p4 --no-mixed -t -x
Bowtie: --phred64 --fr -n0 --best -q -M2 -X1000 -I0 -p2 -t

Bowtie recruits more reads than Bowtie2 in this conditions, but Bowtie2 allows more SNPs (differences from reference genome) than Bowtie. I've represented my data in a graphic. I've selected one region of the genome and I've analysed the coverage and the SNPs (representing it as % of differences from reference sequence). As I have 100 bacteria DNA, I need to see the diversity, and the only way is with the SNPs. I include some of this results.

I don't know by what is happennig...

Thanks for all