Cancer mutations in Tumour and Tumour free

Question

[H.Hasani]

I'm kind of unsure how to biologically interpret mutations found in the tumour of Sample1 , while it exists in the tumour free of sample2! I already have controlled for what might seem like germ-line mutations coming from the same individual.

One could assume there is a contamination (which VERY controlled in our lab), so I'm wondering if there is another explanation?!

Thanks!