I recently read a couple studies that concluded the 25% of genetic similarity between cows and reptiles is actually primarily due to TEs (transposable elements) rather than common ancestry.
Here's the link to the study for more information: https://www.theatlantic.com/science/archive/2017/10/how-a-quarter-of-the-cow-genome-came-from-reptiles/542868/
Now, I'm a strong believer in evolution, but I'm wondering if there's even the slightest possibility that the 97-99% number floating around when it comes to human and chimp/bonobo genetic similarities isn't exactly accurate, especially with the existence of TEs. I supposed my question is, simply put, could TEs serve as an alternative explanation to common ancestry for humans and modern apes? Also would this undermine the ERV/retrovirus remains argument as well?