"The current gap filling state contains data with qualifiers" helper informs the user that some of the chemicals used for the prediction have data with qualifier (i.e. data with not exact value, e.g. >3%, <10%, etc.). 

When data with qualifier is included in the prediction, their absolute value is taken. 

When you make manual read-across or trend analysis you can remove these data by following steps:

1. Click on Calculation options;

2. Click on Data usage;

3. Select All;4. Click on OK (Figure 1).

Figure 1

Once all data points are on the matrix, click on  Select/filter data (1) and then Filter points by test conditions (2) (Figure 2). Data filter window appears. Go to Data Relevance section and select Qualifiers (3). You can see if some of your data points have any type of qualifier. Mark all different qualifiers (4) by click on them consecutively with pressed Ctrl button and click on Remove (5) to eliminate all data points which have not exact data value.

Figure 2