Figure 5: Distribution of non-reference matching bases per genome position after reads alignment by Pipeline A. The dotted line represents the fraction of local coverage that is any non-reference base, the solid black line is the maximum of the identical non-reference bases that have at least one read in both the forward and reverse directions, and the red line represents those variants meeting the criteria of the black curve, but further confirmed in 3 replicate, statistical identical, read sets. The continuum of the fractions is indicative of population structure and criteria of SNP calling threshold, as those variants exceeding a fraction of 0.5 (the consensus).