In order to attribute phenotype to a genotype it is important to know that all relevant sequence differences were detected. False negatives (i.e. failures to detect mutations that are actually present) can result in erroneous interpretation, especially considering that a single mutation can have a dramatic impact on phenotype. False positives on the other hand (i.e. the reporting of sequence differences that are not actually present) are not a big problem in most cases since even 100 false mutations can be checked and refuted with PCR amplification and Sanger sequencing for less money than a typical resequencing experiment.