Roof leak

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The base flashing is not on top of the shingles. It is installed as it should be. The bottom part does go over the shingles at the bottom. Some get fancy and muck a tab over the flange at the bottom, but that only creates a damn for the water coming down the sides to back up against. The silicone all over everything is not needed if done properly. The only place there should be silicone is around whee the pipe meets the base flashing and around the storm collar.

The OP's is installed correctly. doug crane's post was a response to my observation in the post before his.
 
I have read this entire thread and am not sure who has said what about the silicone. However, all of the silicone around the base of the flashing, where it meets the shingles, should not be there. It is not necessary and may cause a leak. If presented with the job of finding this leak, the first thing I would do is remove the flashing and all the gooped up silicone, then install the flashing properly. The shingles should be trimmed so that they do not contact the vertical part of the flashing. The silicone is not necessary and could cause damming and a leak. I am not saying that the silicone is necessarily the problem, but it could be, and should be the first thing eliminated. Then go from there. As others have said the leak could be from higher on the roof, but I just don't like the looks of all that silicone where it is.
 
Agree with the above except I do see two mistakes. Exposed nails is a peave of mine. There is no reason to expose any nails on the entire roof except for the last piece of ridge cap. Those nails are potential leaks that will allow a surprising amount of water in. Not usually at first but after a few years.

The second mistake is not leaving enough gap between the shingles and the cone of the flashing. You need a good inch there. Any less and junk will accumulate and water will back up under the shingles.
 
And of course that silicone is a hack job. No extra silicone should be used. Just what came from the flashing factory.
 
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