In figure 2, it shows the where the retrocopies of the genes were found. The lines are colored according to the chromosome of their source gene, and the black dots show insertions. The other end of the line shows where the retrocopied gene is inserted and found (together with its name). However, the black dots(insertions) appear to stand on the place of the source gene(the one that got copied but remained in place), instead of the retrocopy gene(thus the >inserted< one). I've talked with some people about it and could only come to the conclusion that the black dots are placed at the wrong end of the lines.
Thanks for pointing this out, and sorry this post hasn't come to my notice any sooner than just now - as others in this thread have worked out, the legend should indeed read "Discordant read mappings are represented by links colored based on the chromosome of the insertion". Will look into getting a correction submitted for the legend.
It does appear that their legend is wrong. The lines aren't colored by the chromosome of the source gene, but by the chromosome of the insertion location (at least for Cox7c and Matr3, the only ones I checked). Having said that, the dots do appear to show the approximate insertion location.
I would recommend checking the genomic location of a couple additional genes and then it should be clear.
Thank you for checking it out. That does indeed appear to make more sense than misplaced insertions, when looking at the picture. Also checked out several genes for their location to affirm it.
If you get a chance, please email the authors about this. If my interpretation is correct, they can just have a little correction issued for the paper so that the legend doesn't trip anyone else up.
Before any of us look at the paper, have you tried emailing the authors to ask?
No sorry. I would have done normally, but I'm out of time, so I hoped to get some quick responses here.