Extract mapping coverage from GTF files
So consider this, you know how many reads map to each of your genes (1). Does that tell you anything about (2) the number of reads that mapped against non-gene regions (3) the number of reads that did not map against the genome at all? 

If you only use the gtf files, you know the number of (1) but not of (2) and (3). To me it sounds like you would want to do something as described in this post.

What it boils down to is:

Finding out how many (unique) reads are mapped, counting pairs once

samtools view -F 0x4 foo.sorted.bam | cut -f 1 | sort | uniq | wc -l


Counting how many total reads you have. Since you have paired-end data the number of forward reads suffice:

cat forward_reads.fastq | grep '@' | wc -l


The percentage is then simply mapped_reads/total_reads