Your question is a valid one — one that many winemakers before you have wondered about. As you have discovered, where you take a sample from in a tank can give you varying readings and you find yourself wondering which reading is the most accurate. The specific gravity (or degrees Brix, or Baume, depending upon the scale you use) of a juice or wine is dependent upon many things, all of which have to do with the density of a solution. The denser the solution is, the higher one’s hydrometer will float, and the higher the apparent level of sugar in the juice or wine.
Since temperature affects density (the colder something is, the more dense it is), the temperature of a solution must be taken into account and corrected? in order to get an accurate reading.Typically, a fermentation is warmer on top and cooler on the bottom as the warmer fermenting juice will tend to rise. Furthermore, if your wine is fermenting on the skins, the floating “cap” of skins will be even hotter than the fermenting juice below and will create their own fermentation “micro climate.” The warmer a fermentation is, the faster it will go to completion so, naturally, if you haven’t mixed up your container in a while, a top sample will have a lower SG reading than a bottom sample. Similarly, as density is a measure of soluble solids, any solids, soluble or insoluble, in the sample will contribute to the appearance of density. This means if you take a bottom sample out of the valve in your container, it will most likely be nice and thick due to the settling of solids, even during fermentation(lees). This extra material will do nothing but make your hydrometer float higher, giving you a poor picture of what the whole vessel is doing. If you take a sample from the top, you will run into the afore-mentioned cap, rank with its own thick floaty bits, which you will have to judiciously strain out in order to get a good reading.
The solution? Mix your vessel well, take a sample from the top of the vessel (or if your vessel has a drawing-off point that’s not right on the bottom, use that) and strain it in order to get any floating skins, stems, leaves that might disrupt your reading. (A coffee filter in a kitchen strainer works great for this.) Always correct for temperature and you should have a pretty accurate picture of how your SG is doing.
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