Tophat multiple alignment result in different mapping rates

[anlin00007]

Hello,

I am using tophat to map the ribosome profiling data. First I limited the multiple hits report up to 2, which is:

-g/--max-multihits <int> = 2

Then, I changed this parameter to 5, with no more other changes. However, from the align_summary file, I can see the mapping rates increased, which means more reads mapped to the reference. Based on the tophat manual, this parameter should just change the number of multiple hits in the report which has no effect on the alignment?

I am confusing why the mapping rate changed.