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Is it possible for two different layers, both based on the same shapefile, to include different features?

I seem to have two layers (using QGIS); one shows some points, and the other shows different points; yet they seem to have the same layer source.

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    Check source in layer properties, also check attribute tables. If its only visible difference, maybe its just different styling of duplicated layer.
    – Oto Kaláb
    Feb 26, 2017 at 17:29

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If you have two layers pointing to the same shapefile they will both have access to exactly the same features. However, there are ways to have those two layers displaying different sub sets of features. One way is to define a feature filter on the layer (right click on the layer, select Properties, and click on the General tab, look at the bottom of the dialog), which is a query that specifies which features in the shapefile will be displayed. Another would be to define a thematic symbolization that excluded some of the features. You can check the Layer Source (at the top of the General tab on the Properties dialog) to see if the two layers are actually pointing to the same shapefile.

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