The above section provides alternative allele frequency (AAF) information for selected variant cross-provincial populations or genetic subgroups whose genomes as well the variant have been included in the database. In the AAF distribution map, each provincial or genetic subgroups part is filled with special colors which represent the allele frequency for a population. Specific values of allele frequency and the number of each genotype can be obtained from the figure by hovering the cursor over the area or selecting display mode ‘Data’ in the top right corner. We provide multiple different types of datasets, which can be queried by selecting from the drop-down menu of ‘Dataset’.

The above section provides the variant browser surrounding the location. Bases, genes, and alleles from one sample of CHB are displayed.

This section provides alternative allele frequency (AAF) information for selected variant cross ancient genomes included in the database. In the AAF distribution map, each pie represents the allele frequency for an ancient population. Users can custom the populations, data sets and ancestries to show or not show the corresponding pies. By hovering the cursor over each pie, it returns you the population name that the pie represents and gives you the frequencies and genotypes in detail. By dragging the slider ‘Period’, users can select ancient populations of different periods. By switching figures to the table in the top right corner, the web returns the detailed information in table format. Note that if there is no pie in the map, that means the selected variant does not exist in the included ancient genomes, suggesting the variant either was not covered (not callable) by those genomes or the variant is reference homozygous.

This section provides the effects, such as variant types, genes and impact of the selected variant. The annotation was performed by the variant effect predictor (VEP). To see the variant type description in detail, please go to the following link: https://asia.ensembl.org/info/genome/variation/prediction/predicted_data.html

This section provides conservation scores for the selected variant and the underlying principle is that the functional importance variant is evolutionary conserved. Currently, the annotation includes phastCons, GERP, SIFT, polyPhen-2, and CADD scores. Each score has its value system and threshold, based on which the consequences of variants can be estimated.

This section summarizes the population differentiation between eastern and western Eurasian populations measured by FST (ranging from 0 to 1). The FST values between population pairs were shown in the figure. A higher FST value (close to 1) suggests that the eastern and western Eurasian populations show higher differentiation in the selected variant, while a lower value (close to 0) indicates the similarity of the selected variant between eastern and western Eurasian populations. Users can obtain specific allele, allele frequency, and FST values by hovering the cursor over each variant.

This section provides the natural selection signals for the searched variant and its surrounding region. Three different methods are performed: FST, iHS and neutrality tests. Users can download each figure or table at the top right corner of the specific figure or table. For the method of ‘FST’, pairwise populations can be selected by users (NEH: Northeast Han, CCH: Central China Han, NWH: Northwest Han, SEH: Southeast Han, SWH: Southwest Han, SCH: South Coast Han).

This section provides genomic diversity patterns for the selected variants or their surrounding regions. Users can select the length of region and methods. Currently, the database includes pairwise difference (pairDiff), heterozygosity, haplotype diversity (haplo), and nucleotide diversity (nucloeo) to estimate diversity. The calculation is in real-time. Heterozygosity is variant-based, while the other methods are all region-based.

The above section provides a genetic linkage pattern for the selected variant and its surrounding region. Users can change the length of the region window and methods.

The above section provides the haplotype structure pattern for the selected variant and its surrounding region. Haplotypes are sorted by their frequency. Blue blocks represent reference alleles and red blocks represent alternative alleles. Users can change the length of the region window and the filter condition of minor allele frequency (MAF).