Wrong number of mapped reads in TopHat2 output

[Mchicken]

Hey guys,

I ran TopHat2 for paired-end data with "-g 1", so if there are multiple alignments with the same score, only one of these is reported randomly.

Here my TopHat2 output (align_summary.txt)

Left reads:
Input : 80531201
Mapped : 58052831 (72.1% of input)
of these: 564717 ( 1.0%) have multiple alignments (852074 have >1)
Right reads:
Input : 80531201
Mapped : 38820447 (48.2% of input)
of these: 564717 ( 1.5%) have multiple alignments (683388 have >1)
Unpaired reads:
Input : 275828
Mapped : 127812 (46.3% of input)
60.1% overall read mapping rate.

Aligned pairs: 28004530
of these: 564717 ( 2.0%) have multiple alignments
27873421 (99.5%) are discordant alignments
0.2% concordant pair alignment rate.

So there are 58,052,831 forward reads aligned and 38,820,447 reverse reads aligned. So in my sam file I should have 96,873,278 reads.

But actually I observe 96,885,173 reads in the sam file. So there are 11,895 reads in the Sam file, not present in the TopHat2 output. I observed this mistake (?) in 7 other libraries.

Do I miss something? Or is this an error of TopHat2.

Thanks for your suggestions.

Mario