[galaxy-user] illogical results in Tophat2 analysis

Hello, I used a Tophat 2 analysis and got 99.2% discordant in the summary, while in fact I checked the distance between the reads and got 170 with std of 35 (this is the data i filled in the Tophat2). Why did the Tophat2 test found 99.2% discordant when it should have been much lower? The starting reads was 16665209, in a Bowtie2 test i got a logical outcome of 16567482, while on the other hand i got from Tophat2 35066991 and 34816158 - not logical. I tried to do the same test number of times with another data and got resemblance in the results. In all of the tests in Tophat2 i got discordant 99% and higher. What am i doing wrong? What is the correct way to feed data into the test? Thank you Si.