This is a test version of Biostars. For the public version, visit https://www.biostars.org.
discrepancy between reads

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

enter image description here

igv reads bam deletion
• 1,979 views • link
updated by swbarnes2 swbarnes2 • written by n.mekkes • n.mekkes

Thank you, this does seem to be the case!

• 1 views • link
written by n.mekkes • n.mekkes

If an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accepted. You can accept more than one if they work.
Upvote|Bookmark|Accept

Please use ADD COMMENT/ADD REPLY when responding to existing posts to keep threads logically organized.

• 1 views • link
written by GenoMax GenoMax

2 answers

Looks like a hemizygous deletion.

• 1 views • link
written by Devon Ryan Devon Ryan

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

• 1 views • link
written by Nicolas Rosewick Nicolas Rosewick

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.

• 1 views • link
written by swbarnes2 swbarnes2

Log in to answer this question.

More posts like this