Haplotype block-fitting analysis. Starting from estimated allele frequency differences for each individual single nucleotide polymorphism (SNP) from pooled genotyping, we use linear regression to solve for frequency differences of the underlying common haplotype patterns. In this example, we show a hypothetical haplotype block consisting of six SNPs and three common haplotypes. Measured frequency differences are shown for the haplotype tagging alleles for each SNP, which are also indicated by boxes in the haplotype patterns. In this example, we are estimating two free parameters from six SNP measurements, since the three pattern differences are constrained to sum to 0. Thus, these pattern differences should have lower variance than the individual SNP measurements. From the pattern differences, we are able to estimate the true allele frequency differences for each SNP more accurately.