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The y-value shown in indexLabel and toolTip depends on yValueFormatString and other properties like toolTipContent, contentFormatter may over-ride the value shown in toolTip. Setting indexLabel, toolTipContent / content properties properly should work fine in your case.
If this doesn’t solve the issue you are facing. kindly share JSFiddle with sample data so that we can look into the options that you are using, understand the scenario better and help you out.