Sequencing information is used to correlate alleles at certain locations to alleles at other locations. The statistical information from the reads of fragments in a sample can be used to determine the phasing of haplotypes and to correct or confirm based calls at the locations. In one example, a confidence value (strength score) is determined for a particular hypothesis, which can include whether two alleles are on a same haplotype at two particular loci, as well as what the alleles are on another haplotype (e.g. for a diploid organism). The strength can include a positive contribution from data that is consistent with the hypothesis and a negative contribution from data is that inconsistent with the hypothesis, where both values can be used in a formula to determine the strength.