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

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