The apple pictured is a of the Gala variety,typically striped.The stripes swirl around a brown protrusion. The protrusion is flexible,in the way a leaf is flexible. The flesh underneath is not discolored or soft. The apple is not misshapen,the seeds are not un-developed or underdeveloped. 
What is this brown protrusion called and what causes it?
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$\begingroup$ Did it grow on/next to a branch? $\endgroup$– a coderMar 18, 2018 at 22:24
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$\begingroup$ I don't know. It was sold loose it a supermarket. I only saw it after it was picked. $\endgroup$– peterMar 28, 2018 at 18:34
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1 Answer
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I take it that the question is about the mis-shapenness of the apple, that the stick we see in the dip is the core. The morphology (shape) of fruits such as apple and pear are very sensitive to how well the fruit was pollinated. As we know there can be a variable number of seeds in an apple, but the important fact determining shape is that there should be viable seed develop in each of the five seed pockets resulting in balanced development of the fruit. If the pollination is poor and only a few embryo seeds are fertilized, then the development of the surrounding flesh will favour the pockets that contain viable seed, resulting in possibly mis-shapen fruit. Once you have wondered enough and decide to eat, cut open carefully and on the small side you should see that the seeds are either too few, non-existent or failed to develop.
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$\begingroup$ Not sure what you mean "the stick we see in the dip is the core". I have seen this odd thing few times before on apples, but usually a little less extreme than in peter's picture. In the ones I have seen, the apple isn't really mis-shapen. It just has a small flexible, as peter calls it, "protrusion" on the side. The structure inside the apple seems completely normal, and the stem, core, and seeds look fine. I think this little blemish is really just a surface phenomenon. ...However, I certainly don't know what it is or what causes it, so I am curious to see if there are any other answers. $\endgroup$– Lorel C.Mar 19, 2018 at 3:13
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$\begingroup$ Thats right, Lorel C. My question is about the brown thing on the side of the apple, not misshapeness. $\endgroup$– peterMar 20, 2018 at 14:56
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$\begingroup$ I don't know what part of the tree it grew on.It was sold loose,in the supermarket. $\endgroup$– peterMar 20, 2018 at 15:08