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Where is your sample coming from? Is there a possibility of contamination? If yes, from which source.
The samples are from patients and were checked for contamination with none found. Thank you for your help!
While the percentage can be much higher you have what you have. Are you using a splice-aware aligner? You can take a look at the reads that did not map by checking a few with blast @NCBI (unless you have already done this by "were checked for contamination").