Hello Hisae,
Unfortunately if you often sell only one big ticket item (or similar prices of items at a time) the deposit will always or often always be the same.
The solution would be to use a table which is similar to double entry accounting. The first is the deposits (and running total) of deposits in your bank. The second would be the payouts Export from Shopify. By adding a running total to this you can compare that all deposits exist, or by which amount it is off (ie last pay out or last two payouts, depending on the time of day etc). Totals by week or month or even a running total will make this much more clear.
A second idea comes from my experience. I have noticed the delay between payout is identical (this is my personal experience with my home bank in Canada, so your experience may vary by banking institution). I can tell if the payout is scheduled for a specific day, which time it will arrive and it is quite predictable and follows national holidays. If your bank follows this it can be another simple way to verify and validate similar deposits.