Discrepancy between mosdepth coverage and bam profiles on IGV
Hi there,
I have an ONT bam file that i ran mosdepth for coverage using this:
$MOSDEPTH --fast-mode -t 4 $SAMPLE $NGMLR_BAM 
I plotted the coverage per region and in my region of interest i see this huge spike up 
![image](https://user-images.githubusercontent.com/53702866/145609445-24116e55-580f-497b-b72a-a3ab91c8b6ee.png)

However, this does not correspond at all with the bam profile on IGV - in fact it's the oppposite- barely any reads in the region showing very high coverage.
![image](https://user-images.githubusercontent.com/53702866/145609246-1850b62d-1e1b-49ff-bfaa-bb3992ded082.png)


I wonder if anyone has come across this? Do you have any ideas as to why this occured?
Thanks!
A

