tophat2 aligment ratio reduced when increase insert size

[huan]

Now I have two set of HiSeq pair end equencing data for the same sample with different insert size(196 and 225). The I use tophat2 to align the reads to the genome seperately, the tophat2 parameter (--read-mismatches 2,--read-edit-dist 2,--max-intron-length 5000000,--library-type fr-unstranded,--mate-inner-dist 40) is same. But the overall read mapping rate is different(insert size 196: 90%,insert size 196: 80% ). What's the reason for this different? What can I do for this(such as change the tophat2 parameter)?

Thanks a lot for any advice.