Confusions about SV results

[qiuyixmm]

Hello,
I used reciprocal alignment to compare A genome and B genome by mummer, and then identified structual variarions by nucdiff. The SVs were considered as reliable results whose breakpoint coordinates , in two rounds of aligenmet and identification, were same in A and B genome separately.
However, the SVs regions in A genome were not consisdent with those in B genome. For example, NucDiff identified a 200 bp deletion located in exon region of Gene A in genome A, while the corresponding insertion fragment in genome B was not located in Gene A region in most case. It is normal for SV identification?

[kseniakh]

Since I know too little about your genomes and haven't seen the results, it is quite difficult for me to say if it is normal or not. In general, if the corresponding fragment in B is not located in Gene A, it may mean that Gene A and corresponding fragment are quite similar and mummer have chosen this fragment as the best option for the alignment.

[qiuyixmm]

These two genome are from different but closely related species. A genome was downloaded from NCBI and B genome is a de novo assembly in our lab. The mummer results show colinearity is high between these two species. The high similarity between corresponding fragments and genes is possible. It is may be not the main factor becasue these conflicts can be deteced in most case. I checked different types of SVs ( insertion, deletion and inversion ) manually. I don't find a satisfactory results. Gene features of SVs between two genomes usually can not be mathed in my project.