Abstract: In accordance with some embodiments, systems, methods, and media for classifying genetic sequencing results based on pathogen-specific adaptive thresholds are provided. In some embodiments, a system comprises a processor programmed to: receive negative control results, each comprising values indicative of a number of reads detected in the respective negative control sample for an organism; generate a model based on the negative control results; receive a clinical sample result for a clinical sample, comprising values indicative of a number of reads detected in the clinical sample for an organism of a plurality of organisms; identify, utilizing the model, any values in the clinical sample that are likely to be diagnostically significant; generate a report based on the clinical sample result and organisms associated with a value likely to be diagnostically significant; and cause the report to be presented to a user.