[IGV] Is it an aneuploidy ?

Question

[slfksdjfsdls]

It is marked "first in pair" and "second in pair" depending on the selection (on the Y chromosome)

The F2R1 can also change to F1R2

It also does that on the X chromosome

Is it an aneuploidy ?

Answer 1

[d-cameron]

The read pair you can posted looks completely normal for 2x151bp sequencing of a 270bp long DNA fragment.

Is it an aneuploidy ?

Aneuploidy requires more than just a single read.

The F2R1 can also change to F1R2

All at indicates is which strand the fragment was sequenced from.

It also does that on the X chromosome

Your data probably does this on all chromosomes. Also, are you aware that there are pseudoautosomal regions on X and Y?

It is marked "first in pair" and "second in pair" depending on the selection (on the Y chromosome)

That is also completely normal for paired-end sequencing data.

Overall, your question is very unclear. I strongly recommend to you read up on some review papers on structural variation to gain a better understanding of the nature of both NGS data, and genomic rearrangements.