> For the complete documentation index, see [llms.txt](https://help.connected.illumina.com/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://help.connected.illumina.com/emedgene/emedgene-analyze-manual/variant_page/population_statistics_section.md). # Population statistics tab The **Population Statistics tab** displays population allele data across various ethnicities in [public](#public-population-data-sources-per-variant-type) and [internal databases](/emedgene/emedgene-analyze-manual/settings/organization_settings_-330+/workbench-and-pipeline/organization-db-management/organization-databases.md). ## The Highest Allele Frequency per Demographics badge The **Highest Allele Frequency per Demographics** badge above the table summarizes how common the variant is in control populations. The category is based on the higher of two values: [**Max AF**](#max-af) and [**Emedgene DB frequency**](#emedgene-db-frequency) divided by 5. | Badge | Resulting value | | ---------------- | --------------- | | **Private** | 0 | | **Rare** | > 0% and < 1% | | **Low freq** | ≥ 1% and ≤ 5% | | **Polymorphism** | > 5% | ### Max AF **Max AF** is the highest alternative allele frequency reported for the variant in any public population frequency database. {% hint style="warning" %} **Note** Not to be confused with **gnomAD** **Max AF** in the [**Summary tab**](/emedgene/emedgene-analyze-manual/variant_page/summary_section.md#population-summary). That value uses gnomAD only: for each ancestry group, exome and genome counts are combined, and there is no AN > 1000 cutoff. {% endhint %} Emedgene checks each of these [sources](#public-population-data-sources-per-variant-type) on its own. From each source it takes that database’s overall frequency and each ancestry group’s frequency. It then reports the single highest of those values. {% hint style="info" %} MITOMAP has no ancestry groups: one frequency per variant is compared, with no AN cutoff. {% endhint %} An ancestry group is used only if it was genotyped in more than 1000 alleles (AN > 1000). Groups with AN ≤ 1000 are omitted so a very small slice cannot inflate **Max AF**. gnomAD exomes and gnomAD genomes are treated as separate sources. Ancestry groups are compared individually. East Asian in 1000 Genomes, East Asian in gnomAD exomes, and East Asian in gnomAD genomes are three different measurements; they are not merged into one East Asian frequency, and the same group in two databases is not averaged. Isolated or founder groups — Finnish (FIN), Ashkenazi Jewish (ASJ), Amish (AMI), and Middle Eastern (MID) — are included when that database reports them. The overall frequency of a database is also compared. It mixes all groups in that database, so it is typically lower than the highest group. It can still be the reported **Max AF** if the highest group has AN ≤ 1000 and is excluded. ### Emedgene DB frequency **Emedgene DB frequency** is the frequency in the Emedgene internal database. Dividing by 5 keeps internal data informative without letting it categorize a variant as common on its own. If the variant is present in public databases, **Max AF** almost always determines the badge. If the variant is absent from public databases, the **Emedgene internal frequency** must reach 5% to reach **Low Frequency**, and exceed 25% to reach **Polymorphism**. ## Population Statistics table The **Population Statistics table** displays one row per population: **European**, **African**, **Asian**, **Latino**, **Middle Eastern**, **Other**, and **Organization DBs**. Each row shows aggregated metrics across databases. Select a row to view metrics broken down by population and database. Displayed metrics depend on the variant type. ### Non-mitochondrial variants Aggregated metrics per row: * **Highest Allele Frequency:** Highest allele frequency across databases, displayed as `AF (AC/AN)` * **# of Homozygotes:** Combined homozygote count across databases Expanded row details: * **Allele frequency** * **Alternative allele count** * **Homozygote count** * **Total** (allele number)
### Mitochondrial variants Aggregated metrics per row: * **Highest Homoplasmy Frequency**: Highest homoplasmy frequency across databases * **# Heteroplasmy Count**: Combined heteroplasmy count across databases * **# Homoplasmy Count**: Combined homoplasmy count across databases Expanded row details: * **Homoplasmy frequency** * **Heteroplasmy count** * **Homoplasmy count** * **Total** (allele number)
## Public population data sources per variant type
Variant typePublic databases
SNV, MNV (v100.39+), indelgnomAD, 1000 Genomes, ExAC, ESP 6500
mtDNA SNV/indelgnomAD, MITOMAP
DEL, DUP, INS, TRA (v100.41+), INV (v100.41+)gnomAD SV, 1000 Genomes, Decipher, DGV
STRgnomAD STR, 1000 Genomes
LOH/ROH, Haplotype, BND (v100.41+)Not available
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