transcript alignment generated with gffread against the reference

[Dzamuk]

Hi, after generating the transcript file with gffread I decided to align it back against the reference that resulted only in 84.38% overall alignment rate. How come? Why do I get 704 reads that were not aligned? Is it because of exon-exon junctions in the transcript?

gffread -w refs/transcripts.fa -g refs/22.fa refs/22.gtf
IDX=refs/22.fa
hisat2-build $IDX $IDX
hisat2 -x $IDX -f -U refs/transcripts.fa | samtools sort > refs/transcripts.bam

4506 reads; of these:
4506 (100.00%) were unpaired; of these:
704 (15.62%) aligned 0 times
3703 (82.18%) aligned exactly 1 time
99 (2.20%) aligned >1 times
84.38% overall alignment rate