reason for low mapping rate??

[miaom]

we did RNASeq using HiSeq 2000 100PE. When the data were back, I mapping them to the reference sequence, but got very low mapping rate (30-40%). I asked around, some people suggest to checked for adaptor contamination.
I run Trimmomatic and FastQC again. There is almost no improvement. The report and figures are as follows. Could anybody help with the problem?

#---------------
PASS Basic Statistics A_1.fq
PASS Per base sequence quality A_1.fq
PASS Per sequence quality scores A_1.fq
PASS Per base sequence content A_1.fq
PASS Per base GC content A_1.fq
WARN Per sequence GC content A_1.fq
PASS Per base N content A_1.fq
WARN Sequence Length Distribution A_1.fq
FAIL Sequence Duplication Levels A_1.fq
WARN Overrepresented sequences A_1.fq
FAIL Kmer Content A_1.fq
#---------------
Figures:
per_base_quality.png,
kmer_profiles.png,
per_sequence_quality.png,
duplication_levels.png
.

[Torst]

DNA or RNA?
What organism?
Fresh, frozen, FFPE ?

[mihuzx]

maybe something wrong with the library construction.
can map the reads to ncbi db or rRNA db to check if the library is pure and no rRNA.
I am sorry my English is poor.Hope i made it clear.

[rnaeye]

Did you check if unmapped reads mapping to something else such as external contamination etc?