Figure 4

Comparison of SNP density plots before (“Top” allele definition; black line) and after (“Plus” allele definition; red line) GACT conversion. The SNP density was measured per 500,000 bp window. It is clear that the SNP count (or density) increase after GACT converts all the mismatched loci, e.g., from 61.05 (median) to 117 SNPs per window. Moreover, it is evident that the increase is not biased with regard to physical location, which indicates that the allele definition mismatches are uniformly distributed across the chromosome. The dotted horizontal lines represent the median of values of each line matched by color. The median, instead of mean, was used since the former was less vulnerable to outliers (e.g. zero counts in the centromere region). The “Forward/Reverse” allele definition showed a similar distribution of mismatches with the 1000 Genomes, however, only the “TOP” definition is shown due to its higher level of mismatches (51.5% mismatches in “TOP” versus 21.7% mismatch in “Forward”). Other chromosomes showed similar patterns, and thus only the results of chromosome 1 are shown.