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Table 2 Summary of variant annotation types and their web illustration elements

From: PGG.SNV: understanding the evolutionary and medical implications of human single nucleotide variations in diverse populations

No. Annotation Description Illustration
0 Basic information Basic information, such as allele status, alternative allele frequency of all genomes as a whole, and variant-related links Card
1 Variant browser The Integrative Genomics Viewer (IGV) to visualize genomic data sets, such as human and ancient reference genomes, and conservation scores IGV browser
2 Population prevalence Alternative allele frequency (AAF) in worldwide populations AAF distribution map; Table
3 Ancient frequency Alternative allele frequency for selected variant in ancient genomes AAF distribution map; Table.
4 Variant effect Variant types, effects, and gene contents for selected variant Table
5 Consequence prediction Consequence predicted Conservation scores for selected variant Table
6 Population differentiation Estimation of population differentiation that measured by FST Heat map plot; Table
7 Natural selection Natural selection signals for selected variant and/or its surrounding region Manhattan plot, Table
8 Genomic diversity Genomic diversity pattern for regions near selected variant Scatter plot, Table
9 Linkage disequilibrium (LD) Genetic linkage pattern for regions near selected variant LD decay plot; Table