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Background  High-throughput sequencing is a cost effective method for identifying genetic variation, and it is currently in use on a large scale across the field of biology, including ecology and population genetics. Correctly identifying variable sites and allele frequencies from sequencing data remains challenging, in large part due to artifacts and biases inherent in the sequencing process. Selecting variants that are diagnostic is commonly done using diversity statistics like  F ST  , but these measures are not ideal for the task.    Results  Here, we develop a method that directly calculates the expected amount of information gained from observing each variant site. We then develop and implement a conservative estimator that takes into account uncertainity introduced by sampling bias and sequencing error. This estimator is applied to simulated and real sequencing data, and we discuss how it performs compared to the commonly used existing methods for identifying diagnostic polymorphisms.    Conclusion  The expected information content gives an easy to interpret measure for the usefulness of variant sites. The results show that we achieve a clear separation between true variants and noise, allowing us to select candidate sites with a high degree of confidence.

Estimating the information value of polymorphic sites using pooled sequences