Figure 1

A comparison between traditional approaches and our strategy of SNP identification. Panel A shows two homeologs (duplicated chromosomes) and the sequence of both alleles from each chromosome. The fish are homozygous and only have one allele from each homeolog. This means that SNPs can only be found by comparing sequences between the two homozygous fish. Any variation found within a fish is a paralogous sequence variant (i.e. the first nucleotide in the gene sequence). Panel B illustrates the differences between traditional approaches and ours. The traditional approach would scan every nucleotide position and identify any variant as a possible SNP. This leads to a 50% error rate for the illustrated case (SNP1 is actually a paralogous sequence variant). Our approach uses windows of sequence to identify potential SNPs. Variant windows, in this case 9 nucleotides, are compared between individuals, with windows found in both individuals not considered for SNP identification.