With reference to your concerns about references, the place to start is with your job interview. If you sense that a reference might voice negative comments about you, the best step is to bring up the issue yourself during the interview. This allows you to give your side of the story, place the information in the framework that you desire, and remove the element of surprise. By doing so, the impact of any negative comment can be significantly decreased.
The larger issue is that the reference checker is unlikely to get any information at all from a supervisor at your prior company. Most companies today refer all reference checks to one individual, generally a Human Resources representative if the company has one. The typical guideline is that employers will only verify job title and dates of employment. There can be significant exposure for employers who go beyond these boundaries.
Either way, if a potential employer asks permission to check your references, you should grant it. If you refuse to let a potential employer contact a previous employer, that could be perceived more negatively than a negative reference.
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