Sou you have a new flapper. Try this clean the flush valve this is where the flapper seals and you have to make sure that it rest on the center of the flush valve.They make different sizes so you have to make sure you have the right one. One more thing adjust the chain and make sure it has enough slack to let it rest all the way down on the flush valve.
You can all so do a test hold down the flapper and see if the water still leaks.
And make sure the the line that goes in the over flow tube is not to far down in this tube it should just be in far enough in the holder to keep it in place.
The tube and collar are one piece so it should not leak there if it is leaking there then you will need a new one and they dont coast that much.
Do you have this type of flapper
If so I would try this type of flapper
The bolts just tighten the tank to the bowl and keep the water from leaking onto the outside of the bowl when flushed. this has nothing to do with the water leaking into the bowl.
You see the nut in the photo above that tightens the flush valve to the tank if this is not tight then the water would only leak on the outside of the tank not inside the bowl.
So if you have a flapper with a float then I would try one without a float and you can not just take the float off you would need a new flapper.
If the tank had a hairline crack the water would be all over the place and not going into the bowl.
First off this is good news.
And you can tighten more but I would put some plumbers putty on.
To do this you would remove the overflow tube and put plumbers putty around the tube before you put it back through the tank then re tighten the nut and this should stop the leak.