After going through your data, I see where this is happening.
There is such a range of data, on the high end you have 16,777 and on the very low end you have 2,343. The graphing library always needs to have a lower bar for spacing which is why it's adding the -5000.
2343 is actually right on the threshold of the algorithm for this. You can see in the first image the -5000 exists (because it increments by 5000 and 2343 is less than 2500)
But in this image, I've changed the value to 2500 and the -5000 axis is gone