Sometimes when I do comparisons, I see a
~ as a value.
It appears to indicate that the value is "not available".
From Search Console Help - Search Analytics Report - Comparing your data:
If you compare two groups, and a value is very rare in one group but not rare in the other group, the rare group will show ~ for that row to indicate that the number is not available. For example, if you compare query impressions between Germany and Thailand, the result row for "Deutsche Bundesbank" will probably show an impression number for Germany, and a ~ (not available) for Thailand. This is because the impression count for Thailand is at the end of a very long tail of results. It does not necessarily mean zero, but it is far down the list for that group. However, if you filter by the rare value (in this example "Deutsche Bundesbank"), you should see data values for both categories.
Downloaded data unavailable/not a number values. If you download the data in the report, any values shown as ~ or - (not available/not a number) on the report will be zeros in the downloaded data.