I was audited a few years ago, although it wasn't from my daytrades, but rather from not including my employee option trades in my Schedule D (taxes are taken out in the W-2 but you still need to put the sales in the Sched D). From what I understood talking with the IRS guy, they compare the gross proceeds from all the 1099's with your schedule D total. If the numbers are off a certain amount, the computer kicks it out and a human takes a look. I don't know if they ever really look at your individual trades but if the gains looked out of whack, I wouldn't be surprised if you'd get an audit.
The audit itself was no big deal, BTW. I received a letter requesting me to visit the local office with my Schedule D and 1099s and trade information. I spent a morning there talking to the guy as we both tried to figure out why the numbers were off. Surprisingly, this IRS guy knew amazingly little about how stock options were supposed to be reported -- I had to explain to him what I had read on the subject on irs.gov.
This was a few years ago, but he didn't have a summary of all my trades, just a stack of paper with each individual transaction recorded on a separate page. I'm not kidding, we had to use my only documentation of my trades because what he had was useless!
Anyway, as long as you don't do anything dishonest, audits are no big deal. I probably know more about how to successfully cheat the government know that I know what they look for -- probably not the purpose of auditing me! LOL
Disclaimer: above is not legal advice, just my own experience.