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valueFormatString formats the labels appearing on axisY. To format the y-values that appear in toolTip / indexLabel, you should use yValueFormatString. Setting yValueFormatSting to ‘#,##0.00’ should work fine in your case. Please refer documentation on yValueFormatString for more info and formatting options available for the same.
It would be helpful for us to understand your scenario better when we look at your working code live in jsfiddle. So I kindly request you to create jsfiddle and share it with us, rather than pasting code, if you are still facing any issue.