Such a SNP is therefore less likely to be a false SNP due to sequencing errors in one or more of the reads in the contig resulting in a better in silico assessment of polymorphism and consequently a more polymorphic one when assayed at the population level.
Thirteen out of 16 markers were polymorphic, one marker was monomorphic, and two markers amplified unreliably (Table 1).
Of the 32 primer pairs tested, 15 were polymorphic, one was monomorphic, and 16 failed to amplify the expected products.
For I. shikokianus, seven loci were polymorphic, one locus was monomorphic, and amplification failed for two loci.
Of the 28 loci tested, 26 loci (93%) were polymorphic, one (3.6%) was monomorphic, and one (3.6%) did not amplify for all samples under these conditions.
The corresponding region in P. falciparum and P. vivax proved to be likewise the most polymorphic one in many studies [ 14, 20, 30– 30].
Since promoter regions are often polymorphic, one would expect under optimal conditions to be able to recover an eQTL at the genomic location of many of the examined target transcripts.
Duplicated markers identified in the haploids (Table 1) during database development were used for mapping when one of the paralogs was polymorphic (one paralog polymorphic, parental genotype aa and ab, or aa and bc) or when both paralogs were polymorphic for different alleles (both paralogs polymorphic, parental genotype ab and ac and ab and cd).
In a second step, a labelled target produced for each Ae. aegypti individual as described in the first step was hybridized to the library fragments spotted on a glass slide in order to reveal the polymorphic ones.
Unique SNP markers were distinguished from the polymorphic ones, defined as being diagnostic for a single cultivar (Singleton).
