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

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 F_ST

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