mapped vs. aligned in TopHat and flagstat

[PFS]

Sorry if this is a silly question.

Assuming here mapped ~ aligned.

My understanding is that TopHat output contains only alignment information. Therefore, not all input reads make it into the output, because not all reads align.

Can I conclude that because the unmapped reads don't make it in the Tophat output, the flagstat tools will always return 100% of reads mapped on a tophat output?

[Jon_Keats]

That is correct

[PFS]

Thus, considering a tophat output (BAM format), why do I see reads with flags that indicate the reads are unmapped? Is that because those unmapped reads have a mate that is mapped ?