Mapping to reference shows HIghest peak in other area than IR region(chloroplast GEnome)

Question

[siva.claude]

I have done with chloroplast assembly to annotation.And I found IR Region based Reference data. When I do reconfirmation of IR by mapping to Reference(raw data).. the highest peaks shows up in other area than IR region. Do I have mis-assembled seq or is that anything else that I can do verify IR region? recommendation any tool to identify the IR region?