When I execute a simple statement in phpMyAdmin like
SELECT *
FROM a
where \"a\" has 500\'000 rows, it gives me a time of a few milliseconds on
Imagine you have a pretty big table, let's say a million rows. Now you do a select, something you know is going to take a while:
SELECT * FROM bigTable WHERE value > 1234
...and PMA will report (after some waiting) that the query took some 0.0045 seconds. This is not the whole query time, this is the time of getting the first 25 hits. Or 50, or whatever you set the page size to. So it's obviously fast - it stops as soon as you get the first screenful of rows. But you will notice that it gives you this deceptive result after looong seconds; it's because MySQL needs to really do the job, in order to determine which rows to return. It runs the whole query, and then it takes another look and returns only a few rows. That's what you get the time of.
Do a count() with the same conditions.
SELECT COUNT(1) FROM bigTable WHERE value > 1234
You will get ONE row telling you the total number of rows, and naturally, PMA will display the exact time needed for this. It has to, because now the first page and the whole result means the same thing.