Fig. 2: Marker property outputs within the discovery pipeline. | Nature Communications

Fig. 2: Marker property outputs within the discovery pipeline.

From: Lineage-informative microhaplotypes for recurrence classification and spatio-temporal surveillance of Plasmodium vivax malaria parasites

Fig. 2

Panel (a) illustrates an example marker selection plot output from the marker selection framework. Panel (b) illustrates examples of marker heterozygosity and distance distributions output from the marker selection framework. Panel (c) illustrates the chromosome distribution of three panels (two of which were selected within the framework) that were evaluated for their capacity to reconstruct parasite relatedness. Two new microhaplotype panels were created from the microhaplotype discovery pipeline, named “Random mhaps” plotted in orange, and “High-diversity mhaps” plotted in purple. These two panels were selected to have 100 microhaplotype markers using windows that were well-spaced and had between 3–10 SNPS, with even distribution across all 14 chromosomes and a minimum diversity with heterozygosity ≥0.65. The markers for the Random mhaps panel were selected randomly without optimisation, while the High-diversity mhaps panel were optimised to have the highest heterozygosity possible in each region. These two high-resolution panels were compared to the commonly used biallelic 42-SNP panel, named “BR38” in green. Only 38 markers of this panel are considered informative and included in this representation.

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