Question about plot interpretation; large putative inversion

[jphruska]

Hello --

Thank you for developing and maintaining a powerful resource for the genomics community.

I've genotyped SVs for a species of bird, and noticed there was an aberrantly large inversion that I suspected was a false positive. To check, I produced a samplot image for individuals of the three genotypes (0/0,0/1,1/1). The genotypes of each individual are indicated.

I have a few questions regarding interpretation. First, for inversions, is there a diagnostic for discriminating between the three genotypes (such as is done with differences in read coverage for deletions)? For example, would the number of discordant paired-end reads spanning the inversion be suggestive of different genotypic states?

Secondly, it appears the main signal of an inversion here is a single pair of discordant reads? Am I interpreting this correctly? If so, there appears to be a single pair of reads that is consistently mapping to the same locations on the reference genome, regardless of the called genotype? There also appears to be a second pair of discordant reads for COL_52524, but that doesn't seem to be in support of an inversion?

Any suggestions on how to best interpret these results would be greatly appreciated.

Thanks Jack