Thank you for the well thought out and thorough feedback, this helped me immensely! I worked back through the program paying special attention to layout. I also noticed I said the 5th element when indeed it was the fourth element, or 3rd array slice, that corresponded to chromosome locus.

Currently the revised program will print the correct number of output files and increments the position and placeholder variables correctly :). All the files are blank because, as you said, start and end values don't change so the test is always FLASE. This is because the starting locus in my data sits at the 2.6 million mark, while $start = 1 and $end = 1,000,001

It seems unnecessarily convoluted but also within the scope of my perl knowledge base to assign two more place-holding variables to $start and $end respectively, incrementing them within the else loop when the test is FALSE. I think this will work but I have to think about how to accomplish this. Thanks again, Ken.