The discrepancy between the bowtie2 alignment summary and the samtools flagstat

Question

[daffodil]

Hi, I have used bowtie2 command and I got this summary for alignment:

16182482 reads; of these:
  16182482 (100.00%) were paired; of these:
    12338467 (76.25%) aligned concordantly 0 times
    3194611 (19.74%) aligned concordantly exactly 1 time
    649404 (4.01%) aligned concordantly >1 times
23.75% 

But when I used samtools flagstat to see the stat of alingment I got this report :

qPRO300kClip_S1.sam
^[[O^[[I7688030 + 0 in total (QC-passed reads + QC-failed reads)
7688030 + 0 primary
0 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
0 + 0 primary duplicates
7688030 + 0 mapped (100.00% : N/A)
7688030 + 0 primary mapped (100.00% : N/A)
7688030 + 0 paired in sequencing
3844015 + 0 read1
3844015 + 0 read2
7688030 + 0 properly paired (100.00% : N/A)
7688030 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with m

It would be appritiated if any body know about this discrepancy between the bowtie2 alignment summary and the samtools flagstat. Best regards