In our simulation this strategy had the lowest FNR in many settings (see Figure 2 for example), therefore we believe some of these uniquely identified variants are legitimate variants that were missed by the other two strategies.
Artifacts specific to this approach include the difficulties inherent in performing variant discovery via interspecies mapping since there is significantly more legitimate variation between the reads and the reference sequence due to interspecies variation.
At every site where there are reads that differ from the reference genome, the probability that these reads contain legitimate genetic variants and not sequencing errors or technical artifacts is calculated.
Regardless, this result suggests that of the 3.67 million heterozygous variants identified in the autosomal, non-repeat regions of the UMD3.1 reference, as many, or more than, 2.94 million (3.67M×0.8) of them are legitimate intraspecies variation.
But names that are Middle Eastern, Pakistani, Indonesian or Indian very often have numerous variants, all legitimate.
(Part II, "The Four Winds") But this soon taxes the patience of the reader, who is never entirely convinced that the inevitable metrical variants are legitimate: Sent the melons and tobacco, And the grapes in purple clusters.
As a significant percentage of samples in each experiment are processed in duplicate (to enable stringent marker selection based on scoring reproducibility), all sequence variants that are not legitimate SNP markers are filtered out.
Of these, only one was a legitimate SNP: rs28943580 resulting in a R258C variant.
This argument forms the core of intelligent design, a neocreationist movement seeking to establish certain variants of the design argument as legitimate science, rather than as philosophy or theology, and have them be taught alongside evolution.
