René's URL Explorer Experiment

{"@context":"https://schema.org","@type":"DiscussionForumPosting","headline":"Question about plot interpretation; large putative inversion","articleBody":"Hello --\r\n\r\nThank you for developing and maintaining a powerful resource for the genomics community. \r\n\r\nI'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. \r\n\r\nI 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? \r\n\r\nSecondly, 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?\r\n\r\nAny suggestions on how to best interpret these results would be greatly appreciated. \r\n\r\nThanks\r\nJack\r\n![4_14676614_57494906](https://github.com/ryanlayer/samplot/assets/26208838/fb51d6d0-e89b-4d79-b4f0-b0a1d0538b8f)\r\n\r\n\r\n","author":{"url":"https://github.com/jphruska","@type":"Person","name":"jphruska"},"datePublished":"2024-05-31T17:26:03.000Z","interactionStatistic":{"@type":"InteractionCounter","interactionType":"https://schema.org/CommentAction","userInteractionCount":3},"url":"https://github.com/198/samplot/issues/198"}