Does these Cuffcompare results look okay

[KnowNothing2]

I aligned my RNAseq data to the mouse mm10 genome using Bowtie2. I then generated a GTF file using Cufflinks, and then used Cuffcompare to compare against an annotated mouse genome (from UCSC Table Browswer).

# Cuffcompare v2.1.1 | Command line was:
#/home/adam/cufflinks/cuffcompare transcripts.gtf -r refFlatMouse.gtf
#

#= Summary for dataset: transcripts.gtf :
# Query mRNAs : 13129 in 13129 loci (0 multi-exon transcripts)
# (0 multi-transcript loci, ~1.0 transcripts per locus)
# Reference mRNAs : 30786 in 23311 loci (27576 multi-exon)
# Corresponding super-loci: 3150
#--------------------| Sn | Sp | fSn | fSp
Base level: 2.5 68.1 - -
Exon level: 0.1 2.3 1.2 20.3
Intron level: 0.0 -nan 0.0 -nan
Intron chain level: 0.0 -nan 0.0 -nan
Transcript level: 0.0 0.0 0.0 0.0
Locus level: 0.0 0.0 0.0 0.0

Matching intron chains: 0
Matching loci: 0

Missed exons: 206087/216519 ( 95.2%)
Novel exons: 2718/13129 ( 20.7%)
Missed introns: 193970/193970 (100.0%)
Missed loci: 20087/23311 ( 86.2%)
Novel loci: 2718/13129 ( 20.7%)

Total union super-loci across all input datasets: 5887