In what case there are RR reads but no LL reads when detect inversions using IGV?

[Jingfang]

Hi all,
from Integrative Genomics Viewer User Guide (Paired-end alignments - IGV Desktop Application), when an inversion shows up in paired-end reads, there should be both RR reads and LL reads. As shown below.

When I use the orientation of Illumina paired reads to detect inversions, I found a region only have RR reads, see the picture below. I used color alignments by pair orientation, and view mate region in split screen. I don't know what situation would cause this. Looking forward to getting help.

[fchatonnet]

Dear Jingfang, I do not know exactly what may cause this behavior, but I notice that you are performing HiC. Are you sure that you are really looking at the mate region and that the mate reads of you RR reads are not mapped somewhere else in the genome?
It could be that in addition to an inversion, there is also a translocation or another genomic event which disturbs the pairing of reads.
Another idea: did you align the reads by pairs or as single-reads (meaning: did you discard read pairs in which one of the read was not aligned, or did you keep all aligned reads even if they were not paired after alignment)? Could it be that the LL reads paired with the RR reads you're showing were not aligned? If you have an "unmapped.bam" bam file, it could be worth looking at it to see if you can retrieve some mate reads from the RR reads shown here.
Good luck!

[Jingfang]

Dear fchatonnet, thanks for your reply. It's not HiC, they are resequencing reads, and were aligned to reference genome by pairs. I will think about if it is a combination of inversion and another structural variant. For "unmapped.bam", I don't think it is worth looking at, but I will try. Thanks again.