Reasons why genome coordinates may not have a relative between reference genome assemblies

Question

[Atu]

I was wondering why might it be that a given coordinate in say, hg19, may not map to any coordinate in hg38. I have observed that, and I would like to know which are the reasons, conceptually, that may cause the loss of a given coordinate when a new assembly is built. Also, and I guess related to this, I wonder why might a several coordinates from an assembly collapse into a single one in a different one.

Answer 1

[harold.smith.tarheel]

The simplest explanation is that the one reference contains more assembled sequence (i.e., is larger) than the other, so the coordinate does not exist in the smaller reference. Similarly, a larger interval of multiple coordinates can collapse into a single coordinate in the smaller reference (or repetitive regions in the larger one may have been represented only once in the smaller assembly).

Answer 2

[Atu]

Thanks for your answer. As I read it I realize my question was not detailed enough. As the reason you have explained for the case where multiple coordinates may collapse, I meant to ask about biological reasons that may explain the discrepancies mentioned in my question. Thanks!