Reads mapping to different chromosomes at a locus

[Vivekananda Bhat]

Dear friends,

I am looking at the IGV data from a WGS sample. Intron 1 of GNPTAB is showing multiple reads with different colours. What I know is that each color represents the chromosome at which the mate of the read has mapped. Wanted to know why there are so many coloured reads at this position? Could this be repetitive element insertion.

Thanks in advance

Best regards,

Vivek