" in thebelow we can see few rows of a bed file from bowtie2"
Does bowtie2 produce a bed file? As far as I'm aware it produces a SAM file. Please be specific as to where you got your bed file from.
Did you look at the forth column? That appears to be the difference between each of the three repeated entries for each start stop combination.
" anyway i am with yeast and i used tophat2 using ensemble gtf file and so on)"
Be specific as to what commands you've ran already - reproducibility is key.
bamtobed will produce a bed file from a bam file with chromosome, start, stop, read IDs, etc. I guess your followup question would be "but what about gene annotation?" - Look at the biomaRt package