Reads mapped to exonic, intronic and intergenic regions

After the alignment step I checked the rnaseq metrics of all the samples. Among 40 samples three samples show high percentage of reads mapped to intronic regions. What could be the reason?

Samples   Exonic            Intronic    Intergenic
Sample1 545479 (12.8%)  2512309 (58.8%) 1217201 (28.5%)
Sample2 372836 (8.3%)   2556934 (56.8%) 1573032 (34%)
Sample3 529618 (7.3%)   3934615 (54.5%) 2750720 (38.1%)


I also see that 35-40k genes among 58k genes having "zero" read counts. Is this due to contamination? What could be the reason? What does reads mapping to exonic, intronic, intergenic tell?

Update: I used hisat2 for alignment. I used human genome "grch38_snp_tran" from hisat2 website. Libraries were generated using ribosome depletion kit.

• How did the overall alignment rate of those samples compare to the others that had more reasonable intronic alignment rates? May 7, 2018 at 19:40
• I see that all the 37 samples have overall alignment rate between 90-96% and for those 3 samples it is 69%, 79%, 70% overall alignment rate. May 7, 2018 at 20:12
• Sounds like you have degraded samples May 7, 2018 at 20:16
• U mean those 3 samples are degraded? What I should do now? Should I remove them for further analysis? May 7, 2018 at 20:34
• It’s a likely cause, but regardless you should exclude them. May 7, 2018 at 20:35