BAM file: RNEXT read mate map to another position

[Notorious]

Dear All,

I am analyzing a PE RNAseq experiment . Looking at the resulting sorted bams, I have noticed that some of the aligned reads map on another reference (e.g. in the attached figure, the other read map on chrM).

Any idea on what can cause this mismatch? Could it be raise problems during reads counting?


Bam files are obtained as follows:

PE fastq are checked with FASTQC (good overall quality)
PE fastq are aligned to mm10 genome index using hisat2 (mean overall alignment rate >97%)
samtools is used to convert sams to bams, sort and index them.

Thank you very much for your help.