discrepancy between reads

Question

[n.mekkes]

Hello,

Im a beginner who downloaded a tumor BAM file into IGV. When I look at a region having a deletion, I see around 30 "red" read pairs, meaning the distance is greater than expected. The other 50 reads or so are normal grey. There is a clear drop in coverage in this region, but it doesn't completely disappear. How can only some reads have the deletion, while others don't? Im thinking about the homologous chromosome maybe doesn't have the deletion, or maybe DNA from multiple cells in one sample?

Thanks if you have any other ideas

link to figure(hope this works) https://ibb.co/i4bjpz

[ATpoint]

A screenshot would help. Please see How to add images to a Biostars post.

[n.mekkes]

Thank you, this does seem to be the case!

[GenoMax]

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Answer 1

[Devon Ryan]

Looks like a hemizygous deletion.

[Nicolas Rosewick]

Yes only one allele seems to have the deletion. The other not.

Answer 2

[swbarnes2]

Im thinking about the homologous chromosome maybe doesn't have the deletion, or maybe DNA from multiple cells in one sample?

Either explanation could be the right one. It might be tricky to know which is correct.