Using shell = True can be a security risk if your input data comes from an untrusted source. E.g. what if the content of your mid variable is "/dev/null; rm -rf /". This does not seem to be the case in your scenario, so I would not worry too much about it.
In your code you write the result of awk directly to the filename in mid. To debug the problem, you might want to use subprocess.check_output and read the result from your awk invocation in your python program.
cmd = """sort -n -r -k5 %s |
head -n 500|
awk 'OFS="\t"{{if($2-{1}>0){{print $1,$2-{1},$3+{1},$4,$5}}}}'""".format(summit, top_count)
subprocess.check_call(cmd, shell=True, stdout=file)
